https://3decision.discngine.com/blog daily 0.75 2026-03-19 https://3decision.discngine.com/blog/2026/3/12/transforming-structural-biology-research-with-3decision-a-customer-success-story monthly 0.5 2026-03-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ff793dc0-283a-44bf-ac8f-f21a67b8a672/sanofi+logo+big.png Blog - Transforming Structural Biology Research with 3decision®: A customer success story - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/2e975f5f-9201-44f9-83ac-0bc80198d9a9/Untitled+%2830+x+30+cm%29+%28300+x+300+px%29.png Blog - Transforming Structural Biology Research with 3decision®: A customer success story - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1773330932230-YIPW5U4RKNF0UA4X3BDQ/image+%283%29.png Blog - Transforming Structural Biology Research with 3decision®: A customer success story https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1773331008392-V11UO88RSO4OL33XU7HZ/Search_result_page_structure+view.png Blog - Transforming Structural Biology Research with 3decision®: A customer success story https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1773330932195-5IAHY40XXGLSY8SFBA5U/Info-panel_in_3DViewer.png Blog - Transforming Structural Biology Research with 3decision®: A customer success story https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ff793dc0-283a-44bf-ac8f-f21a67b8a672/sanofi+logo+big.png Blog - Transforming Structural Biology Research with 3decision®: A customer success story - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/d8a93690-5e5b-4a2a-b4eb-149d0dc371aa/3decision_RVB_Dark_Horizontal.png Blog - Transforming Structural Biology Research with 3decision®: A customer success story - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/blog/2025/5/14/understanding-glycan-sensitive-vs-glycan-agnostic-pd-1-antibodies-using-3decision-20 monthly 0.5 2025-07-07 https://3decision.discngine.com/blog/2025/4/8/prediction-expertise-and-validation-an-integrated-approach-to-advancing-sbdd monthly 0.5 2025-07-07 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1eacd6b3-f331-4918-a257-b967fbbd5aec/C639A91D-A8AE-4EDD-B62D-37DBE67F447E.jpg Blog - Prediction, expertise, and validation: An integrated approach to advancing SBDD - Make it stand out Darren Green’s talk at Discngine Labs Live: “Optimizing the Impact of Protein Structure Information on Next-Generation Drug Discovery” https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/390df562-0d69-44cd-9d3b-6052f9dd73a0/Optimizing+the+Impact+of+Protein+Structure+Information+v2.png Blog - Prediction, expertise, and validation: An integrated approach to advancing SBDD - Make it stand out Presentation slide from Darren Green referencing the value of structures for drug discovery and development and the need for precise and valid predicted structural models https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ef88eb0b-0764-447a-afbd-67ac05c9b26b/First+page_3decision+brochure+2025.png Blog - Prediction, expertise, and validation: An integrated approach to advancing SBDD - 3decision 2.0 is coming soon! Discover Discngine’s 3D protein structure and data management tool in our new product brochure. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c5769f89-2ec8-437a-a430-299c27ec2477/7BC8068A-4CC4-48E4-B029-5BF335086D0C.JPG Blog - Prediction, expertise, and validation: An integrated approach to advancing SBDD - Make it stand out Discngine Labs Live roundtable session with David Brown (Vertex Pharmaceuticals), Juan Carlos Mobarec (AstraZeneca), Benoit Baillif (Astex Pharmaceuticals) and James Davidson (Vernalis), on “Potential and pitfalls of using computational predictions to drive structure-based drug design” https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/3b77057a-285d-4c48-808d-c99839a52d63/A7C7F703-E410-4CD6-B069-218B198A8F32+%281%29.jpg Blog - Prediction, expertise, and validation: An integrated approach to advancing SBDD - Make it stand out Networking at Discngine Labs Live, Churchill College, Cambridge, UK https://3decision.discngine.com/blog/2025/12/19/discngine-labs-live-setting-new-standards-in-sbdd-experimental-and-predicted-protein-structure-synergies monthly 0.5 2025-12-19 https://3decision.discngine.com/blog/2025/1/10/recent-trends-in-structural-biology-insights-from-the-psdi-conference monthly 0.5 2025-12-02 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/d4aab90d-2ca7-4aa7-96e4-736bb82a2c72/IMG_2487.jpg Blog - What are the recent trends in Structural Biology and Drug Discovery? - Insights from the PSDI conference - Make it stand out Discngine delegation the 32nd Protein Structure Determination in Industry (PSDI) meeting in Paris, France. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1736538891358-AH1VIKGE36OOCZAZXRF2/Discngine+Labs+promo_5.png Blog - What are the recent trends in Structural Biology and Drug Discovery? - Insights from the PSDI conference - Make it stand out Discover event details and join us! https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1736503683988-JGO15PXZ7GM9UQP22BPE/7BA0AEFC-88AD-446F-86DF-93289CBF15F7.JPG Blog - What are the recent trends in Structural Biology and Drug Discovery? - Insights from the PSDI conference https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1736503684820-M8ZVY3YOKV1GUTG5AY09/F386096F-2201-4B17-B62D-2AFEF2D49E85.JPG Blog - What are the recent trends in Structural Biology and Drug Discovery? - Insights from the PSDI conference https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/afa99604-b6fb-43ec-a591-a0e98c2f9cc2/Image1.png Blog - What are the recent trends in Structural Biology and Drug Discovery? 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- Insights from the PSDI conference - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e935e450-e468-4ddc-b6ae-48686dfe88c4/7584579B-91D2-4DB8-98D2-17F7F92A33AE.JPG Blog - What are the recent trends in Structural Biology and Drug Discovery? - Insights from the PSDI conference - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/abbed296-3ac1-4fd5-a504-86175b21554c/case+study+fp_page-0001.jpg Blog - What are the recent trends in Structural Biology and Drug Discovery? - Insights from the PSDI conference - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/blog/2024/11/19/antibody-developability-how-to-effectively-navigate-challenges-and-opportunities-in-predicting-antibody-properties monthly 0.5 2025-12-02 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/242cdd1f-fa76-4439-a39a-a84db1a02197/Picture4.png Blog - Antibody developability: How to effectively navigate challenges and opportunities in predicting antibody properties? - Make it stand out Antibody developability properties https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/d6e5cb45-f0ed-4864-8673-65acec69d009/_3dpredict+COMPUTER_printed+materials.png Blog - Antibody developability: How to effectively navigate challenges and opportunities in predicting antibody properties? - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/47dab8de-ab71-4b3d-8203-0486708b16d9/Essam.png Blog - Antibody developability: How to effectively navigate challenges and opportunities in predicting antibody properties? - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/8ddae63a-7c92-43dd-ba4c-316aef2c7a26/mat.png Blog - Antibody developability: How to effectively navigate challenges and opportunities in predicting antibody properties? - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c9c053fb-7047-462b-ab3e-87d69da001f6/Per.png Blog - Antibody developability: How to effectively navigate challenges and opportunities in predicting antibody properties? - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/abbed296-3ac1-4fd5-a504-86175b21554c/case+study+fp_page-0001.jpg Blog - Antibody developability: How to effectively navigate challenges and opportunities in predicting antibody properties? - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/47dab8de-ab71-4b3d-8203-0486708b16d9/Essam.png Blog - Antibody developability: How to effectively navigate challenges and opportunities in predicting antibody properties? - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/111c10d3-20d0-43ad-813f-a6e7cdf20289/Video3.PNG Blog - Antibody developability: How to effectively navigate challenges and opportunities in predicting antibody properties? - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/blog/2024/8/8/evaluating-protein-protein-interactions-in-af3-predicted-complexes-a-pd-1-case-study monthly 0.5 2025-12-02 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/abbed296-3ac1-4fd5-a504-86175b21554c/case+study+fp_page-0001.jpg Blog - Evaluating protein-protein interactions in AF3 predicted complexes: a PD-1 case study - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/7a755534-b941-4e50-af8b-68a14c52876d/3decision_3dviewer_image+%282%29.png Blog - Evaluating protein-protein interactions in AF3 predicted complexes: a PD-1 case study - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/76e39673-d7e2-403e-a61c-c32f5ebeee18/protein+cell+death+1+with+it%27s+native+ligand.png Blog - Evaluating protein-protein interactions in AF3 predicted complexes: a PD-1 case study - Make it stand out Image 1. 3D structure of the PD-1/PD-L1 complex (PDB: 4ZQK; (6) PD-1 in purple, PD-L1 in orange). The PPI network is represented as dotted lines, and residues involved in the interactions are represented as sticks. H-bonds are in blue, and polar bonds are in yellow. Water molecules are represented as red spheres. The picture is produced using the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/7c855e70-4182-4554-a226-42df8fc088cf/AlphaFol3+orediction+evaluation.png Blog - Evaluating protein-protein interactions in AF3 predicted complexes: a PD-1 case study - Make it stand out Image 2. Evaluation of AF3-predicted model of PD-1P/PD-L1 complex. A) Structure is colored by the pLDDT confidence score of the prediction: blue for very high, light blue for high, yellow for low, and orange for very low confidence. The protein-protein interface in the zoomed-in panel shows very high confidence in the prediction for most of the residues at the interface. The picture was produced using the 3decision® software. B) Display of the Predicted Aligned Error (PAE) for the AF3-predicted PD-1/PD-L1 complex. PD-1 and PD-L1 chains are labeled respectively in purple and orange. The region of PD-1 that is expected to be in proximity to PD-L1 includes residues 20-150, while for PD-L1, the residue range is 20-230. The picture is produced with the PAE Viewer webserver.(10) https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e1223479-8efc-495c-a216-194f8a349da3/Superposition+of+X-Ray+and+alphafold3+model+of+PD-1%2FPD-L1+complex+.png Blog - Evaluating protein-protein interactions in AF3 predicted complexes: a PD-1 case study - Make it stand out Image 3. Superposition of the AF3 model with the experimental structure of PD-1/PD-L1 complex showing high accuracy of the prediction (PDB: 4ZQK; PD-L1 in orange, PD-1 in purple). The view is focused on the protein-protein interface. The picture was produced using the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e33ebe5a-fcde-41c5-87d9-aeab35928056/Protein-protein+interaction+second+hotspot+region+PD-1%2FPD-L1+complex.png Blog - Evaluating protein-protein interactions in AF3 predicted complexes: a PD-1 case study - Make it stand out Image 5. Analysis of the second hotspot region of PD-1/PD-L1 complex. The experimental structure of the complex is PDB: 4ZQK. The PD-1 chain and residues are purple, while the PD-L1 chain and residues are orange. The AF3 predicted model is colored by the pLDDT confidence score. A) PPIs calculated for the experimental structure 4ZQK. Residues involved in the PPIs are labeled and color-coded according to the chain: orange for PD-L1 and purple for PD-1. The water molecule is represented as a red sphere and labeled. B) PPIs calculated for the AF3 predicted model. Labels for the residues involved in the PPIs are color-coded based on the chain. The position of the water molecule observed in the experimental structure is indicated in the red circle. C) Focus on the water-mediated interaction between Ile134 on PD-1 and LTry56 on PD-L1 and the representation of the electron density map of the experimental structure. D) List of residues involved in the analyzed PPIs. The subscript notation “L” before the amino acid indicates residues on PD-L1. Below the table is a legend of the PPI representation: H bonds are represented as long-dashed light blue lines, and salt bridges as long-dashed yellow lines. E) Superposition of the PPI networks for the AF3 predicted model and the experimental structure 4ZQK. The red arrows point to the water-mediated interaction observed on the experimental structure, and the intra-chain interaction between LTyr56 and LGln58 observed for the AF3 model. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/abbed296-3ac1-4fd5-a504-86175b21554c/case+study+fp_page-0001.jpg Blog - Evaluating protein-protein interactions in AF3 predicted complexes: a PD-1 case study - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/blog/2024/5/20/leverage-3d-structures-for-sbdd-projects monthly 0.5 2025-12-02 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/2b3e48e1-48d0-4a53-96a1-b8363fdd5836/Scheme+1.png Blog - Leverage Experimental and in Silico 3D Protein Structures to Accelerate SBDD Projects  - Make it stand out Scheme 1. Chemical structures of bexarotene (1) and compound 2 and reported literature values1 of respective EC50 (for RXRα), aqueous solubility, and cytotoxicity. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/deee47d3-d29f-48ac-9bd2-fd6c54e5a964/Figure+1.png Blog - Leverage Experimental and in Silico 3D Protein Structures to Accelerate SBDD Projects  - Make it stand out Figure 1. 3decision Structure Registration page, “Edit Metadata, General” section. The method used to produce the 3D protein structure in 3decision can be set as X-ray diffraction, Solution NMR, Electron Microscopy, or Model. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/58a0cc7b-d106-4fa4-994e-15bb997336be/Figure+2.png Blog - Leverage Experimental and in Silico 3D Protein Structures to Accelerate SBDD Projects  - Make it stand out Figure 2. 3decision Structure Registration page, “Edit Metadata, Related Structures” section. Relationships between the new structure and other structures already included in the 3decision database can be set from this section. The related structure can be either “Parent” or “Child” of the new structure, and the available “Relation type” options are: Bioassembly, Refined, Derived, or Prepared for Docking. A “Relation description” field is available to provide a supplementary description of the relationship. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/a32b66e8-1d70-4467-8806-df74af070da9/Figure+3.png Blog - Leverage Experimental and in Silico 3D Protein Structures to Accelerate SBDD Projects  - Make it stand out Figure 3. Binding site comparison between docking pose of compound 2 in RXRα binding site (in orange) and X-ray crystal structure of bexarotene in complex with RXRα (PDB ID: 4K6I, in blue). A) Protein-ligand interaction patterns for compound 2 (in orange) and bexarotene (in blue). The grey arrows indicate the salt bridges between the carboxylic acid moieties, the N backbone of Ala327 and the side chain of Arg316. The protein-ligand interactions are calculated by the 3decision® software upon structure registration. B) Representation of the binding site surface, color-coded by hydrophobicity index: from red (hydrophilic) to green (hydrophobic). Surface calculated with the 3decision® software. Hydrophobic sub-pockets targeted for ligand optimization are indicated by the grey arrows. The phenyl ring and chlorine atom on compound 2 are indicated in orange. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/8012f377-d61e-4bc9-aff0-edd084234a28/Scheme+2.png Blog - Leverage Experimental and in Silico 3D Protein Structures to Accelerate SBDD Projects  - Make it stand out Scheme 2. Chemical structures of compound 2 and compound 3 with reported literature values1 of EC50 (for RXRα), aqueous solubility, and cytotoxicity. Compound 3 was produced from compound 2 by structure-driven optimization. The modified substituents of compound 2 are indicated in the dashed lines. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/0db59359-5715-4a5c-bcd6-d8a47cf07c17/Figure+4.png Blog - Leverage Experimental and in Silico 3D Protein Structures to Accelerate SBDD Projects  - Make it stand out Figure 4. Ligand binding model comparison between docking pose of compound 2 in RXRα binding site (in orange) and X-ray crystal structure of compound 3 in complex with RXRα (PDB ID: 8PP0, in white). Protein-ligand interactions are calculated by the 3decision® software upon structure registration. The grey arrows indicate the salt bridges between the carboxylic acid moieties, the N backbone of Ala327, and the side chain of Arg316. The binding site surface, color-coded by hydrophobicity index, is calculated with the 3decision® software. The phenyl ring and chlorine atom on compound 2 are indicated in orange, and the indane and trifluoromethyl moieties on compound 3 are indicated in white. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ebb3901a-2cc9-4976-bbfe-fcdf57fc07d9/Scheme+3.png Blog - Leverage Experimental and in Silico 3D Protein Structures to Accelerate SBDD Projects  - Make it stand out Scheme 3. Chemical structure of compound 4 and reported literature values2 of EC50 (for RXRα), aqueous solubility, and cytotoxicity. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/43c935bd-8b34-428d-9d5e-3e268ea5fdb6/Figure+5.png Blog - Leverage Experimental and in Silico 3D Protein Structures to Accelerate SBDD Projects  - Make it stand out Figure 5. The centralization of 3D protein structures from different sources (e.g., in silico models and experimental structures) in a single repository like 3decision creates a structural knowledge database to exploit for structure-based drug discovery efforts. This maximizes the use of structural data, aiding ideation and lead optimization, ultimately enhancing the discovery of new drugs. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/805ac6cc-ba83-406b-8570-3cd4d7eaa481/Figure+6.png Blog - Leverage Experimental and in Silico 3D Protein Structures to Accelerate SBDD Projects  - Make it stand out Figure 6. 3decision Advanced Search page. On the left, you can search by structure property or chemical structure. On the right, you have the launched queries. The Uniprot Code search for “RXRA_HUMAN retrieved 115 hits, and the Chemistry Search for the exact structure of bexarotene got 2 hits. The two queries combined by the logical operator “AND” (in the orange button) provided a total of 2 structures in the database matching both, as indicated in the blue button “Display 2 Results” on the bottom. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b88555fb-a513-4881-af0c-424b69cd2c59/Figure+7.png Blog - Leverage Experimental and in Silico 3D Protein Structures to Accelerate SBDD Projects  - Make it stand out Figure 7. 3decision Results Navigation page. For each structure a general overview is provided, with information such as: resolution, experimental methos, chains composing the protein, and ligand(s) 2D representation. Easy export of the structure(s) of interest is available. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1d5ec2a0-eb52-4db6-ba20-ef1caefd07f5/Whitepaper%2BFirst%2BPage_final1.png Blog - Leverage Experimental and in Silico 3D Protein Structures to Accelerate SBDD Projects  - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/blog/2023/09/12/how-to-best-exploit-3d-protein-structures-for-ideation-in-sbdd monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1706140721697-501CLDYPLVFDOOHT5QVE/deep+pocket.jpg Blog - How to best exploit 3D protein structures for ideation in SBDD Enhance ideation in SBDD with centralized 3D protein structure repository https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/99289aff-d610-4f16-b7ce-4c3809146a43/chart1.png Blog - How to best exploit 3D protein structures for ideation in SBDD The results of the poll conducted during the Discngine Labs event with a simple question: “What do you use to store your 3D protein structures?” The majority of participants from the pharma industry reported that they are still using Internal folders/Sharepoint to store their structural data. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/2a16bdfa-b1c0-471a-a4db-676650cac591/AlphaFold%2Bbanner.png Blog - How to best exploit 3D protein structures for ideation in SBDD Watch the recording of our previous Discngine Labs with drug discovery experts from industry and academia on the topic: Protein structure prediction: What next after Alpha Fold? https://3decision.discngine.com/blog/2023/08/31/discngine-labs-harnessing-the-potential-of-structural-data-for-ideation-in-drug-discovery monthly 0.5 2024-11-14 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/25570be1-0012-47d7-a2a4-911c1f6ca399/LogosFINAL.png Blog - Discngine Labs Recap: Harnessing the Potential of Structural Data for Ideation in Drug Discovery - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ce699228-8579-4d06-97f9-8eaca4b501db/Simone+Fulle.png Blog - Discngine Labs Recap: Harnessing the Potential of Structural Data for Ideation in Drug Discovery - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/baadaa64-209b-4613-88e1-6b51933f1f2b/Daria+Goldmann.png Blog - Discngine Labs Recap: Harnessing the Potential of Structural Data for Ideation in Drug Discovery - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/296241ac-5760-4811-abc3-be7730babadb/David+Thompson.png Blog - Discngine Labs Recap: Harnessing the Potential of Structural Data for Ideation in Drug Discovery - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/43d534c9-738b-4cc8-b700-26794162c494/Simone+Exsci.png Blog - Discngine Labs Recap: Harnessing the Potential of Structural Data for Ideation in Drug Discovery - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/blog/2023/05/25/understanding-selectivity-of-clk-kinase-inhibitors-structural-insights-with-3decision monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/fb98da4a-3f91-4608-899a-32bd8df314c1/0.+Bauerine.png Blog - Understanding selectivity of CLK kinase inhibitors: structural insights with 3decision® https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/274221da-d3b8-486c-ab7e-326a8cc48d74/1.+Advanced+Search.png Blog - Understanding selectivity of CLK kinase inhibitors: structural insights with 3decision® Figure 1: The query based on the combination of protein family name “CLK” and chemical substructure “dichloro-methyl-indole” in the 3decision Advanced search https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b62e5eb8-2deb-46ec-9315-04b6bf8b9363/2.+Results+navigation+page+-+Structure+view+mode.png Blog - Understanding selectivity of CLK kinase inhibitors: structural insights with 3decision® Figure 2: The 8 CLK hit structures from the query in the “Structure” view mode of the 3decision results navigation page. Click to Zoom In https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c495efd3-b383-4fb4-a2df-8777bdd4786d/3.+Results+navigation+page+-+Ligand+view+mode.png Blog - Understanding selectivity of CLK kinase inhibitors: structural insights with 3decision® Figure 3: The search results in the “Ligand” view mode of the 3decision results navigation page showing the chemical matter found in the hit structures. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/6b23a797-5326-43bd-9a2c-52d74e891693/4.+project.png Blog - Understanding selectivity of CLK kinase inhibitors: structural insights with 3decision® Figure 4: Set up of a reference structure for the collection of structures saved in the 3decision Project. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/cdd48086-1e99-433e-ac7b-cba096b4b852/5.+binding+pose+comparison.png Blog - Understanding selectivity of CLK kinase inhibitors: structural insights with 3decision® Figure 5: ATP binding site for kinases: A) CLK1:bauerine C derivative complex (blue, PDB: 6YTG) non-canonical binding mode, halogen bonds between chlorine atoms (in green) and the hinge region; B) CDK7:ATP complex (orange, PDB: 1UA2) showing the canonical ATP binding mode. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/2fbfff55-838a-4797-8989-bd648724ff27/6.+Superposition_final.png Blog - Understanding selectivity of CLK kinase inhibitors: structural insights with 3decision® Figure 6: Superposition of all the project structures in the 3decision 3D Viewer. The blue (CLK1, PDB: 6ytg) and white (CLK3 A319V, PDB: 6Z2V) have the same non-canonical binding pose (halogen bonds in purple), while the orange structure (CLK3, PDB: 6YU1) shows and ATP-like interaction pattern with the hinge region (H-bonds in yellow, indicated by the orange arrows). https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/9a14c1b4-d4be-43f1-bec1-cc6eeb3e182d/7.+Information+Panel.png Blog - Understanding selectivity of CLK kinase inhibitors: structural insights with 3decision® Figure 7: General information on the CLK3 A319V structure summarized in the 3decision Information panel on the left. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/af7c47e3-59cd-4989-801c-3c68acddc80e/8.+Highlight+mode+DFG-1.png Blog - Understanding selectivity of CLK kinase inhibitors: structural insights with 3decision® Figure 8: Differences between the structures highlighted with the 3decision highlight mode. The residues at the DFG-1 position are indicated in the green circle. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/cf754e8b-fe07-4403-9c26-b9bdec8d9497/9.+Annotation+Browser.png Blog - Understanding selectivity of CLK kinase inhibitors: structural insights with 3decision® Figure 9: The DFG-1 Valine residue of CLK1 is highlighted in red in the 3D structure, using the Annotation Browser. https://3decision.discngine.com/blog/2023/03/13/the-impact-of-alphafold-in-drug-discovery-and-emerging-ml-methods monthly 0.5 2024-11-14 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/a1987c05-ed14-4a6f-a11d-885c8644485c/AlphaFold%2Bmdoel.png Blog - The impact of AlphaFold in drug discovery and emerging ML-methods Comparison of experimental and theoretical structures of bromodomain-containing protein 4 (DeepMind AlphaFold model in pink and X-Ray structure (PDB ID:6CJ2) in blue) showing the accuracy of the AI model. The superposition was done with the 3decision software. Source: 3decision blog post. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c398e33c-24bd-4c83-847d-75cd2d9e790e/chart%2Bfinal.png Blog - The impact of AlphaFold in drug discovery and emerging ML-methods Results of the poll “Have AlphaFold models already helped you significantly in a drug discovery project?” that was conducted on LinkedIn (61 votes) and live during the Discngine Labs event (178 votes). The poll participants are mainly scientists from pharma and biotech, working in the early stages of drug discovery. The results from both polls are plotted together since there were no significant differences in the percentages obtained from the two different sources (LinkedIn: yes 34%; DNG Labs: yes 38%). https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/f26f6072-63cd-4400-b1d4-9435565e53e0/Seth.png Blog - The impact of AlphaFold in drug discovery and emerging ML-methods https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/a7b6b5c5-07f9-4a98-8827-4edad73cce8f/Robbie.png Blog - The impact of AlphaFold in drug discovery and emerging ML-methods - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e6bc6f3a-c38c-4123-b504-14501e8b638d/Christian.png Blog - The impact of AlphaFold in drug discovery and emerging ML-methods - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/761a53d2-1505-4e89-8f2c-d726bb7d26e2/CHARM+example.png Blog - The impact of AlphaFold in drug discovery and emerging ML-methods - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/11805c91-533c-4a02-9b08-a533c30322c4/AZ+example.png Blog - The impact of AlphaFold in drug discovery and emerging ML-methods - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/6d481bc7-5ad6-4a14-b564-bffe925e4f9e/Jola.png Blog - The impact of AlphaFold in drug discovery and emerging ML-methods - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c9a38fb9-cd43-4e23-957d-dbc8415a207d/Andy.png Blog - The impact of AlphaFold in drug discovery and emerging ML-methods - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/blog/2023/01/26/discngine-labs-virtual-reality-for-collaborative-drug-design monthly 0.5 2024-10-09 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/79238afe-f9e5-44d4-8148-d29666019869/Logo+updateF.png Blog - Discngine Labs: Protein structure prediction - What’s next after AlphaFold? AlphaFold speakers https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/7b268edb-4018-4981-a8be-9732ae68bdc6/Seth.png Blog - Discngine Labs: Protein structure prediction - What’s next after AlphaFold? https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c4d26b9f-b7de-4921-adeb-d3428cbdc07f/Robbie.png Blog - Discngine Labs: Protein structure prediction - What’s next after AlphaFold? https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ae909fb2-c796-4b4e-98ca-6abc86838e4f/Christian.png Blog - Discngine Labs: Protein structure prediction - What’s next after AlphaFold? https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/5be36618-e308-4999-b450-4925108dad98/Jola.png Blog - Discngine Labs: Protein structure prediction - What’s next after AlphaFold? https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/fca4e3b1-4abf-414a-8d8a-d80050112a99/Andy.png Blog - Discngine Labs: Protein structure prediction - What’s next after AlphaFold? https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e11010b2-3d42-4573-b218-7934866eb9d6/Sergey.png Blog - Discngine Labs: Protein structure prediction - What’s next after AlphaFold? https://3decision.discngine.com/blog/2022/10/04/discngine-labs-the-future-of-cryo-em-in-pharma monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/18cc3e85-d475-4d8b-a8de-f00b8a17105f/Banner+for+Gather.png Blog - Discngine Labs: The future of Cryo-EM in Pharma https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/fce0caf4-9b42-4c5c-94e5-e2b532c2e5aa/Event+image+final.png Blog - Discngine Labs: The future of Cryo-EM in Pharma https://3decision.discngine.com/blog/2022/10/04/discngine-labs-virtual-reality-for-collaborative-drug-design monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ad04d959-22c6-4ba5-9ed3-ba0013dc98a7/Logos+_+300piNEWBIG.png Blog - Discngine Labs: Virtual Reality for Collaborative Drug Design https://3decision.discngine.com/blog/2022/09/28/the-future-of-cryo-em-in-pharma-event-highlights monthly 0.5 2024-11-15 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/fce0caf4-9b42-4c5c-94e5-e2b532c2e5aa/Event+image+final.png Blog - The future of Cryo-EM in Pharma [event highlights] Picture from the Discngine Labs event “The Future of Cryo-EM in Pharma”. https://3decision.discngine.com/blog/2022/06/20/starting-with-3decision-exploration-of-ikaros-protein-family-a-molecular-glue-use-case monthly 0.5 2024-11-14 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b52039e4-8408-4966-b103-0119c945c369/Picture1.PNG Blog - Starting with 3decision®: exploration of Ikaros protein family – a molecular glue use case Image 1: Search results for the query based on the protein family name IKZF in 3decision Basic search. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/97010981-3231-4ba0-90dd-1afb6194fe62/StructureTable.PNG Blog - Starting with 3decision®: exploration of Ikaros protein family – a molecular glue use case Structure View Mode https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/f2278d1d-15df-410e-a7e4-5c6a7b691bc4/LigandTable.PNG Blog - Starting with 3decision®: exploration of Ikaros protein family – a molecular glue use case Ligand View Mode https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/f03c50f8-d1c9-4d8b-bf39-66f9c6b46321/TargetTable.png Blog - Starting with 3decision®: exploration of Ikaros protein family – a molecular glue use case Target View Mode https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c677b7d0-f3ac-45de-aae8-5e1d33fd24a5/Table.PNG Blog - Starting with 3decision®: exploration of Ikaros protein family – a molecular glue use case Table View Mode https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/f815b3a8-e856-485d-b7c0-1aa6e9982566/MoleculesBLOG1.png Blog - Starting with 3decision®: exploration of Ikaros protein family – a molecular glue use case Image 2: The discovered molecular glue compounds - ALV1 and ALV2 - after several Design-Make-Test-Analyze cycles done by the team https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/48e89ad8-ea70-4631-b47b-0f8eedd80f55/Open6H0F.PNG Blog - Starting with 3decision®: exploration of Ikaros protein family – a molecular glue use case Image 3: Select desired structure for visualization in a click . https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/72724c41-3344-4d08-9dcf-fcaa7c58f5af/ColoringLigand.PNG Blog - Starting with 3decision®: exploration of Ikaros protein family – a molecular glue use case Ligand coloring https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/22381e6d-b22f-4585-a99f-62226221d073/Ikaros+Helios+superpositionBLOG.png Blog - Starting with 3decision®: exploration of Ikaros protein family – a molecular glue use case Image 4: The comparison of cereblon-Ikaros structure (6H0F) and cereblon-Helios structure (7LPS ). Superposition in 3decision is based on the selected pockets. The Highlight mode shows the key difference in sequence - Glycin 146 in Ikaros (in pink ) and Histidine141 in Helios (in blue). https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1e28c5c6-4b23-48aa-ab00-c1f2eb7507d1/helios+GSPT1+superpositionBLOG.png Blog - Starting with 3decision®: exploration of Ikaros protein family – a molecular glue use case Image 5: Superposition of Helios with ALV1 and off-target GSPT1 which shows key residues that hinder the binding of ALV1 to the off-target and thus avoid side effects. https://3decision.discngine.com/blog/2022/05/03/five-advantages-of-3decision-aws-quick-start-for-pharma-and-biotech monthly 0.5 2024-11-14 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ce5caf45-f3c9-4818-867e-9376f107cc5e/Powered-By_logo-stack_CMYK_REV.png Blog - Five advantages of 3decision AWS Quick Start for pharma and biotech https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/6921b177-c4de-40c8-b972-cb0e84f3e8c6/discngine-3decision-architecture-diagram.32031ba58d980c13be8c957450177fe5645bc7db.png Blog - Five advantages of 3decision AWS Quick Start for pharma and biotech Quick Start architecture for 3decision on AWS https://3decision.discngine.com/blog/2022/04/28/confo-therapeutics-selects-discngines-3decision-platform-to-leverage-the-full-potential-of-gpcr-structures-towards-the-development-of-novel-therapeutics monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/123eb418-94fe-46ec-9536-a18885d60155/Confotherapeutics-Logo-white_transparent%2Bbackgr%2B-%2Bsmaller%2B-%2BPNG.png Blog - Confo Therapeutics Selects Discngine’s 3decision® Platform to Leverage the Full Potential of GPCR Structures Towards the Development of Novel Therapeutics https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/fca23413-985a-4754-94ed-b36454629839/Discngine+Logo+Dark+Background.png Blog - Confo Therapeutics Selects Discngine’s 3decision® Platform to Leverage the Full Potential of GPCR Structures Towards the Development of Novel Therapeutics https://3decision.discngine.com/blog/2022/04/05/efficient-biomolecular-structural-data-handling-and-analysis-event-highlights monthly 0.5 2024-11-15 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/7087a061-3f43-467d-8dc2-2ab113deae15/subpocet%2Bsearch.png Blog - Efficient biomolecular structural data handling and analysis [Event highlights] 3decision Interface - structure collection (left), 3D Viewer (right) https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c26d3f79-7ae6-4008-853b-d484858b561b/image+for+the+blog.PNG Blog - Efficient biomolecular structural data handling and analysis [Event highlights] 3decision backend architecture https://3decision.discngine.com/blog/2022/01/13/discngine-partners-up-with-chemaxon-to-enhance-its-3decision-platform-for-innovative-structure-driven-drug-discovery monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/934d9e5f-f816-4ed9-850a-0d6029e0e836/chemaxon+logo+NEW.png Blog - Discngine partners up with ChemAxon to enhance its 3decision® platform for innovative structure-driven drug discovery https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/118bab67-b9ef-4943-aaaf-e20cb1eb0fc7/Discngine+Logo+Dark+Background.png Blog - Discngine partners up with ChemAxon to enhance its 3decision® platform for innovative structure-driven drug discovery https://3decision.discngine.com/blog/2021/12/07/fast-growing-techniques-in-structural-biology-and-their-impact-on-drug-discovery monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c4b32ab3-9f9c-4e11-b965-735e26fcfe1e/GABAa%2Breceptor%2Bresolved%2Bwith%2BcryoEM%2Btechnique%2Bin%2Bthe%2Bresolution%2Bof%2B1.png Blog - 5 fast-growing techniques in structural biology and their impact on drug discovery A GABAA receptor monomer: Cryo-EM resolved structure at atomic resolution, PDB ID: 7A5V.Image is captured in the 3decision 3D viewer. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/23a895f4-2247-48ec-9ca1-dd5df8108b20/Contribution%2Bof%2BX-Ray%2Bcrystallography%2Bto%2Bearly%2Bstages%2Bof%2Bdrug%2Bdiscovery.png Blog - 5 fast-growing techniques in structural biology and their impact on drug discovery Contribution of X-Ray crystallography to early stages of drug discovery shown with crystal icons. Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7179213/ https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/db6866f6-9664-4915-8edd-dd2399351381/Serial%2Bfemtosecond%2Bcrystallography%2Bseries%2Bof%2Bsnapshots%2Bof%2Bphotoactive%2Byellow%2Bprotein.gif Blog - 5 fast-growing techniques in structural biology and their impact on drug discovery SFX produced a series of snapshots of what conformational states the photoactive yellow protein (PYP) goes through after light absorption of the chromophore. Source https://pdb101.rcsb.org/motm/207 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/988001bd-ce5c-434e-b0e4-f24187c96e14/Integrative%2Bmodeling%2Bis%2Ba%2Bvery%2Bpopular%2Btechnique%2Bin%2Bstructural%2Bbiology.jpeg Blog - 5 fast-growing techniques in structural biology and their impact on drug discovery Illustration of hybrid modeling technique. Source: https://www.sciencedirect.com/science/article/pii/S0022283620301054 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1ba97845-7fa2-4894-b98c-c5eebd11838b/Alpha%2Bfold%2Bmodel%2Bof%2BBRD4%2Bcompared%2Bto%2Bthe%2Bexperimentally%2Bresolved%2Bstructure.png Blog - 5 fast-growing techniques in structural biology and their impact on drug discovery Comparison of experimental and theoretical structures of bromodomain-containing protein 4 (DeepMind AlphaFold model in pink and X-Ray structure (PDB ID:6CJ2) in blue) showing the accuracy of the AI model. The superposition was done with the 3decision software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/22095ff4-0241-4a55-ad07-26d59018c645/Poll%2B-%2BWhich%2Bof%2Bstructural%2Bbiology%2Btechniques%2Bwill%2Baccelerate%2Bdrug%2Bdesign%2Band%2Bdiscovery.png Blog - 5 fast-growing techniques in structural biology and their impact on drug discovery Poll - Which of structural biology techniques will accelerate drug design and discovery https://3decision.discngine.com/blog/2021/11/09/structure-and-ligand-based-analysis-how-to-combine-the-best-of-two-worlds-for-driving-compound-design monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/5175d2ef-3b25-4d4d-a31f-0f45e783a9f2/copy1website.png Blog - EVENT HIGHLIGHTS: Structure- and ligand-based analysis - How to combine the best of two worlds for driving compound design https://3decision.discngine.com/blog/2021/09/01/webinar-protein-ligand-interaction-search-discover-3decisions-latest-feature-and-generate-ideas-for-scaffold-hopping monthly 0.5 2024-05-06 https://3decision.discngine.com/blog/2021/03/30/discngine-and-nanome-are-bringing-a-new-dimension-to-protein-structure-analysis monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/def2c366-f9dd-44c4-9b73-324620462d91/Nanome_Logo_Horizontal-White.png Blog - Discngine and Nanome are partnering up to enhance the structure-based drug design experience Nanome_Logo.jpg https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/38530cd0-3d2e-4b2a-8a78-396058549af9/3decision-logo-overdark-vertical-nobg-R.png Blog - Discngine and Nanome are partnering up to enhance the structure-based drug design experience logo.PNG https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1708728188911-T7UBR9IPAQBXPVZYGSG1/Discngine+%26+Nanome+image.png Blog - Discngine and Nanome are partnering up to enhance the structure-based drug design experience - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/blog/2021/03/09/customer-success-story-an-innovative-way-of-organizing-data-how-can-3decision-improve-decision-making-process monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/11c46a52-d4ba-42da-8b8c-1c3df1763c2e/IMG_2279.jpg Blog - An innovative way of organizing data: How can 3decision® improve decision-making process? [Customer Success Story] Profile picture of Manuel Cases Thomas https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/378e4721-e461-42b4-a863-2e2278494bfe/3dec%2Bimage%2Bpillar%2Bfinal.png Blog - An innovative way of organizing data: How can 3decision® improve decision-making process? [Customer Success Story] 3decision interface https://3decision.discngine.com/blog/2021/02/18/starting-with-3decision-allosteric-pocket-detection-in-abl1-kinase monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/7c4d6900-f7dd-48b3-86cd-e277ea5ef386/ceb1d-imageofbcl-abl1kinase.png Blog - Starting with 3decision®: Allosteric pocket detection in BCR-ABL1 kinase BCR-ABL1 kinase (PDB:1IEP). https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/64bf7941-e840-4e64-94ef-cf4ff9c117da/79b02-pocketexplorermapin3decisionshowingdruggablepockets.png Blog - Starting with 3decision®: Allosteric pocket detection in BCR-ABL1 kinase Representation of pocket explorer map with scored cavities (PDB:1FPU). https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ab2b1963-fdbe-40e2-8290-3a22165da882/1d3c7-1iep5.pngpocketexplorermapin3decisionshowingdruggablepockets.png Blog - Starting with 3decision®: Allosteric pocket detection in BCR-ABL1 kinase Representation of pocket explorer map with scored cavities (PDB:1IEP). https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/2b38bd78-dcbb-41a5-ad0b-663f85113039/1ebb1-identifiedallostericbindingsiteofbcr-abl1kinase.png Blog - Starting with 3decision®: Allosteric pocket detection in BCR-ABL1 kinase Superposition of “druggable” pockets in the two analyzed structures. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/8bfee107-4170-4e76-81ad-17c06622ab24/ff0e3-asciminibintheallostericpocketofbcr-abl1.png Blog - Starting with 3decision®: Allosteric pocket detection in BCR-ABL1 kinase The allosteric binding site of BCR-ABL1 with novel inhibitor Asciminib (PDB: 5MO4). https://3decision.discngine.com/blog/2021/02/11/whats-new-in-3decision-20211 monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b3c478c6-8612-41b1-acea-ca44c8de386c/051_EmailAlert1.png Blog - What's new in 3decision® 2021.1? 051_EmailAlert1.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/238e5082-fd60-4002-a7b2-d7a31ce4195c/3decision_HighlightMode.png Blog - What's new in 3decision® 2021.1? 3decision_HighlightMode.jpg https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c7c0a377-5b86-4580-8580-a76e0102b7d4/ligand.1.png Blog - What's new in 3decision® 2021.1? 46a31-ligand.1.jpg https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/f6ee14ca-a80a-4bd8-8167-72cb23c1580f/representation+card+5b7v.1.png Blog - What's new in 3decision® 2021.1? 7a1ae-representation2bcard2b5b7v.1.jpg https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b97d1d16-e2d1-4bd2-995e-fc5931b35aa0/workspace+5xfj11.png Blog - What's new in 3decision® 2021.1? bf8db-workspace2b5xfj11.jpg https://3decision.discngine.com/blog/2021/01/21/spotting-differences-in-large-structure-collections monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/2ad9e9ad-b704-4a02-a5ad-cd82491219fd/38a98-screenshot2021-01-19at08.59.30.png Blog - Spotting differences in large structure collections On the left: chek1 kinase structure (5dls) superimposed to chek2 kinase structure (4bdc) with the default binding-site focused representation. On the right, the focused “difference” mode. All backbone is shown as thin ribbon, unless a major conformational change (or multiple mutations) occurs. All mutations or movements on the amino-acid level are shown as sticks. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/57b3dfac-c53a-42ff-8f49-0bd52573ecd6/d09e2-screenshot2021-01-19at10.39.30.png Blog - Spotting differences in large structure collections Example of showing all the differences on a larger ensemble of structures. All “major” movements get shown as lines or cartoon representation. The binding site is very stable and movements on the protein surface can be observed mainly on two locations. https://3decision.discngine.com/blog/2021/01/19/interview-what-are-the-challenges-for-medicinal-chemists-when-working-with-3d-structures monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/de0d6be2-67ce-4fca-b51a-d2819f80ee2f/7cc37-picforthumbnail1.png Blog - What are the challenges for medicinal chemists when working with 3D structures? - Interview pic for thumbnail1.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1ffba4d9-c8d3-4f3a-b174-7af7c300c3fa/George+Sheppard.jpg Blog - What are the challenges for medicinal chemists when working with 3D structures? - Interview George Sheppard.jpg https://3decision.discngine.com/blog/2020/12/18/webinar5-data-sets-preparation monthly 0.5 2024-02-24 https://3decision.discngine.com/blog/2020/12/18/how-to-speed-up-the-preparation-of-data-sets-for-sbdd-webinar-recap monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/75ab89f8-622a-4f41-93fa-3efe7948b660/WEBINAR+first+page.png Blog - How to speed up the preparation of data sets for Structure-Based Drug Design? – Webinar Recap 29320-capture.png https://3decision.discngine.com/blog/2020/12/09/getting-ready-for-alpha-fold-with-3decision monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/d21e7074-efac-400f-9e85-33b91d7717c6/top%2Bimage.png Blog - Getting ready for AlphaFold with 3decision® top image.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/7e0d751c-a9af-43c1-801e-5ec01c0c9702/numbe%2Brof%2Bentries.jpeg Blog - Getting ready for AlphaFold with 3decision® Current number of entries in RCSB PDB https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ccd85603-e3c5-4a7b-a5f0-363084e5d74d/structural%2Bdata%2Bgrowth.jpeg Blog - Getting ready for AlphaFold with 3decision® Structural data growth in the last 4 years: Computationally generated models (SWISS MODEL repository) compared with experimentally determined structures in PDB https://3decision.discngine.com/blog/2020/10/05/should-medicinal-chemists-use-3d-molecular-modelling-tools monthly 0.5 2025-09-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/afb08734-4fb6-45e4-a053-2e33590affff/9539f-image-asset.jpeg Blog - Should medicinal chemists use 3D molecular modeling tools? 9539f-image-asset.jpeg https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/0cfa2ca2-98b4-4f35-8fc7-a13d0d159d71/a1b16-image.jpg Blog - Should medicinal chemists use 3D molecular modeling tools? image.jpg https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/27126c5e-057a-4c9d-81fa-c130faf44bd1/ac9a9-image2bad.jpg Blog - Should medicinal chemists use 3D molecular modeling tools? Alexis Denis, PhD https://3decision.discngine.com/blog/2020/09/16/interview-discngine-and-userstudio-share-their-point-of-view-on-their-collaboration-about-the-recent-improvement-of-3decisions-user-interface monthly 0.5 2025-09-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ede0986c-3401-49ee-9d14-07df5d3da087/schema+process+UserStudio2.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications The project was conducted in a 7 steps process over a few months period, as proposed by UserStudio, and it turned out very effective. (Credit image: Flaticon.com) https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/241e7941-bc19-4d10-a7b2-744c1a65aaac/Dng+Favicon.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications Dng Favicon.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/8c39b13f-a59b-4019-9fd9-a7ee435ddd59/1.+User+Research.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications 1. User Research.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/448d3861-5dd9-4944-bbf2-81311215743d/User+studio.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications User studio.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/241e7941-bc19-4d10-a7b2-744c1a65aaac/Dng+Favicon.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications Dng Favicon.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/448d3861-5dd9-4944-bbf2-81311215743d/User+studio.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications User studio.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/241e7941-bc19-4d10-a7b2-744c1a65aaac/Dng+Favicon.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications Dng Favicon.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/d757006a-b649-4d07-b59e-b66dc9f77e1d/2.+Esquisse+de+la+vision+cible+.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications 2. Esquisse de la vision cible .png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/241e7941-bc19-4d10-a7b2-744c1a65aaac/Dng+Favicon.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications Dng Favicon.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/448d3861-5dd9-4944-bbf2-81311215743d/User+studio.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications User studio.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1708994324351-7PJK44N1JDPQ2AR2Z358/1.+MedChem+class+.JPG Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1708994322807-S9RA00M0Q3A3I3LVDMLN/3.+Atelier+.jpg Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1708994326516-JLR9YFM1XX327PZ9OGMD/3.+Atelier+IMG_3732.jpg Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1708994339744-68NDLKGZZJQ7L0GU4D5J/4.+Simplification+du+parcours+et+userflow.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1708994350397-BF8ZPH2H5LYMS2YFM14R/5.+Rendu+final+3.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/241e7941-bc19-4d10-a7b2-744c1a65aaac/Dng+Favicon.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications Dng Favicon.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/448d3861-5dd9-4944-bbf2-81311215743d/User+studio.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications User studio.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1708992293876-3356U53MAG5HM6M1KCJ7/cfb6e-5.rendufinal2.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications 5. Rendu final 2.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/241e7941-bc19-4d10-a7b2-744c1a65aaac/Dng+Favicon.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications Dng Favicon.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/448d3861-5dd9-4944-bbf2-81311215743d/User+studio.png Blog - Discngine & UserStudio: Uplifting User Experience in life science research applications User studio.png https://3decision.discngine.com/blog/2020/06/26/webinar4 monthly 0.5 2024-02-27 https://3decision.discngine.com/blog/2020/06/09/3decision-v2-discover-the-interaction-search monthly 0.5 2025-12-19 https://3decision.discngine.com/blog/2020/06/08/3decision-v2-discover-the-subpocket-search monthly 0.5 2025-12-19 https://3decision.discngine.com/blog/2020/06/03/3decision-v2-discover-the-new-ui monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/0eb4a44b-48a3-4529-b452-53a491cf7ce4/05371-workspace_2020.06.1.jpg Blog - 3decision® v2 – Discover the new UI workspace_2020.06.1.jpg https://3decision.discngine.com/blog/2020/04/29/webinar3 monthly 0.5 2024-02-27 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/7ed0b38c-a53b-429a-9193-62f457a3ff64/coronavirus-dark-1200x800-image-webinar.jpg Blog - Webinar: 3decision®: Collaborative research on structural data using 3decision – highlights, upcoming novelties and COVID19 efforts. Peter & Gabriella from the 3decision team https://3decision.discngine.com/blog/2020/04/06/sosei-heptares-selects-discngines-3decision-platform monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/9c7bdad3-068f-437c-a743-cf32f1bffbca/00bd8-annotationbrowser.png Blog - Discngine announces that Sosei Heptares will use its 3decision® software to create an unprecedented structural GPCR chemogenomics platform The Annotation Browser - an interactive layout for sequence and structure annotation analysis in 3decision® https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b7976e97-49f5-4eaa-9005-c4c145c3c7cf/3decision-logo-overdark-vertical-nobg-R.png Blog - Discngine announces that Sosei Heptares will use its 3decision® software to create an unprecedented structural GPCR chemogenomics platform 3decision.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/da17b2be-3a6b-4eb9-a4e8-1f4be7429c3b/b21a0-sosei-heptares.png Blog - Discngine announces that Sosei Heptares will use its 3decision® software to create an unprecedented structural GPCR chemogenomics platform sosei-heptares.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b8802248-73ce-4f9b-b2ed-17bfa0163452/Discngine+Logo+Dark+Background.png Blog - Discngine announces that Sosei Heptares will use its 3decision® software to create an unprecedented structural GPCR chemogenomics platform Discngine-Logo-Couleur-Big-Fond.png https://3decision.discngine.com/blog/2020/04/06/sars-cov-2-3-nsp1-a-detailed-analysis monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/41eb9ccd-2135-4f11-9b8a-046a482a9a33/01325-multiple_alignment_copy1.png Blog - SARS-Cov-2 - part 3 - nsp1: A hopefully more detailed analysis of the cellular saboteur Alignment of SARS-CoV-2 nsp1 and SARS-CoV nsp1. Alignment done with MUSCLE and image generated with JalView. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/9cc59781-c637-431a-85ba-70a3e29de028/f103f-image-asset.jpeg Blog - SARS-Cov-2 - part 3 - nsp1: A hopefully more detailed analysis of the cellular saboteur f103f-image-asset.jpeg https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/16585386-4aac-4665-9520-150c8735e371/4e51e-screenshot2020-03-30at12.55.09.png Blog - SARS-Cov-2 - part 3 - nsp1: A hopefully more detailed analysis of the cellular saboteur Results from a systematic mutational study on SARS-CoV nsp1 reported here. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/0a8cb37b-4482-4970-a127-36e945a31a88/735fd-screenshot2020-03-31at09.41.19.png Blog - SARS-Cov-2 - part 3 - nsp1: A hopefully more detailed analysis of the cellular saboteur The the SARS-CoV nsp1 structure 2hsx opened in the Annotation Browser in 3decision. The focus lies on the annotations from the mutagenesis study mentioned in the table above. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e4d2007b-32da-47e0-955a-65e8c421df9b/b880c-screenshot2020-04-05at18.12.01.png Blog - SARS-Cov-2 - part 3 - nsp1: A hopefully more detailed analysis of the cellular saboteur Unique hit obtained via hhpred using “NKGAGGHSYGADLKSFDLGDELGTDPYEDFQENWNTKHSSGVTRELMRELNGG” (C-ter of nsp1 from SARS-CoV-2) as query. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/500a91db-242a-4065-98df-08ad990f39b2/8977e-screenshot2020-04-05at22.23.09.png Blog - SARS-Cov-2 - part 3 - nsp1: A hopefully more detailed analysis of the cellular saboteur Structure of the yeast RNA Exosome complex (source). Spot the Rrp45/46 complex in the middle (yellow/red). https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e35c145e-58c0-4c6e-9a61-801dcaf4dae8/ec23a-3decision_3dviewer_image.png Blog - SARS-Cov-2 - part 3 - nsp1: A hopefully more detailed analysis of the cellular saboteur Overview of the interaction between Rrp45 (green) and Rrp46 (orange). Open the same view in 3decision here. Based on RCSB structure 2nn6 https://3decision.discngine.com/blog/2020/03/27/sars-cov-2-2-from-the-viral-genome-towards-protein-structures monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b2277f88-2b1a-4537-85e3-49c2dbd1af4b/nCoV_genome+%281%29.jpg Blog - SARS-CoV-2 - part 2 - From the viral genome to protein structures The SARS-CoV-2 genome structure as available on viralzone.expasy.org https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/80a44013-38df-42dd-97d1-cc24a5e8ef4d/genomic+structure+and+phylogenic+tree+of+coronavirus.PNG Blog - SARS-CoV-2 - part 2 - From the viral genome to protein structures Image extracted from a review on coronavirus genome structures from early 2020. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ded87bfd-92aa-449a-b440-e85230120654/Screen+Shot+2020-03-28+at+11.46.18.png Blog - SARS-CoV-2 - part 2 - From the viral genome to protein structures Image taken from here https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/3a70a854-0000-44ec-98bf-c04c06d908d1/Schematic-of-the-replication-cycle-of-Middle-East-respiratory-syndrome-coronavirus.PNG Blog - SARS-CoV-2 - part 2 - From the viral genome to protein structures Taken from a review on the previous MERS-CoV outbreak. Apart from a few details, the current SARS-CoV-2 acts rather similarly. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/48f4e7f0-d7f0-44fe-9790-afdb7e7592c3/Screen+Shot+2020-03-28+at+12.16.29.png Blog - SARS-CoV-2 - part 2 - From the viral genome to protein structures An extract of the non structural proteins (nsp) annotations on the official Uniprot entry of SARS-CoV2’s polyprotein pp1ab. Visualisation from 3decision. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ac6a1f13-66ac-4fcb-a792-49093750aa25/0b64a-screenshot2020-04-01at09.10.23.png Blog - SARS-CoV-2 - part 2 - From the viral genome to protein structures Interaction map from https://www.biorxiv.org/content/10.1101/2020.03.22.002386v3 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/566add1c-5233-4da6-a3b2-a6e78cb7206c/Favirapir.png Blog - SARS-CoV-2 - part 2 - From the viral genome to protein structures Screen Shot 2020-03-29 at 14.54.02.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/fcb51b60-3166-41fe-9491-0dc6bde90548/Ribavirin.png Blog - SARS-CoV-2 - part 2 - From the viral genome to protein structures Screen Shot 2020-03-29 at 14.55.37.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/a0075241-4c02-4266-9ee0-6018c0f1a3d8/Remdesivir.png Blog - SARS-CoV-2 - part 2 - From the viral genome to protein structures d30c5-image-asset.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/96855099-a531-409b-a391-c80579330918/galidesivir.png Blog - SARS-CoV-2 - part 2 - From the viral genome to protein structures 24a5b-image-asset.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/90305d26-a10c-40a4-b77b-8a09a9cb1cae/Screen+Shot+2020-03-29+at+15.10.08.png Blog - SARS-CoV-2 - part 2 - From the viral genome to protein structures Screen Shot 2020-03-29 at 15.10.08.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c2bbfcbb-e75d-4f6a-b670-34555a987a49/Chloroquine.png Blog - SARS-CoV-2 - part 2 - From the viral genome to protein structures Screen Shot 2020-03-29 at 15.12.19.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/135dce72-c1ee-4e78-81b6-ced98ff6d3b6/Nitazoxanide.png Blog - SARS-CoV-2 - part 2 - From the viral genome to protein structures Screen Shot 2020-03-29 at 15.19.09.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/6e4b1fb8-dbeb-4cfc-a304-27f4760b5362/disulfiram.png Blog - SARS-CoV-2 - part 2 - From the viral genome to protein structures 807a3-screenshot2020-03-29at15.12.19.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/55918cfc-3478-4354-b09a-45fb95586282/Lopinavir.png Blog - SARS-CoV-2 - part 2 - From the viral genome to protein structures Screen Shot 2020-03-29 at 15.23.32.png https://3decision.discngine.com/blog/2020/03/27/sars-cov-2-1-thriving-for-a-systematic-target-and-hit-id-effort monthly 0.5 2024-05-06 https://3decision.discngine.com/blog/2020/02/18/creating-acollaborative-platform-for-structure-based-drug-discovery monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/33b0b95c-cea6-4485-b645-692c5a49439b/751ba-collaboration.jpg Blog - Discover 3decision® - Part 2: Creating a collaborative platform for Structure-Based Drug Discovery collaboration.jpg https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c67e99d9-a68c-4d83-823d-94efb1705770/a492c-3decisioninterface.jpg Blog - Discover 3decision® - Part 2: Creating a collaborative platform for Structure-Based Drug Discovery 3decision interface.jpg https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/7fc6c4d2-ca7c-4c85-94aa-b5fd469ae53f/Picture1.png Blog - Discover 3decision® - Part 2: Creating a collaborative platform for Structure-Based Drug Discovery lead op loop.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/58c1c12b-6959-4f45-82a0-ef23af3276ae/a51b1-bioit2baward.jpg Blog - Discover 3decision® - Part 2: Creating a collaborative platform for Structure-Based Drug Discovery bioIT+award.jpg https://3decision.discngine.com/blog/2020/02/07/ncov-structurally-speaking-part-2 monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/028b454f-c003-4747-85b0-329f1466c83d/image+1.png Blog - 2019-nCov, structurally speaking - part II Figure 1. The peptide-like inhibitor N3 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/8bac1f8e-b965-4bf3-aa8f-361f5e4f5e69/image+2.png Blog - 2019-nCov, structurally speaking - part II Figure 2. the newly resolved structure of the 2019-nCoV main protease in complex with a peptide-like inhibitor (PDB 6lu7). https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/2520ab90-54cb-4c96-a9f1-cba08b330bad/image+3.png Blog - 2019-nCov, structurally speaking - part II Figure 3. The 3decision Sequence Viewer. To the left: Sequence alignment of the 2019-nCoV and SARS-nCoV orf1ab polyprotein sequences. Only the residues in the active site of the Mpro are shown. Differences compared to the reference sequence (here: 2019-nCoV) are shown by one-letter codes. Only one residue differs – S3309A. To the right: X-ray structure of the 2019-nCoV Mpro (6lu7) with the residue S3309 highlighted. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/16ef6ff8-165c-45c5-930f-765fbde2b940/image+4.png Blog - 2019-nCov, structurally speaking - part II Figure 4. Overlay of three 2019-nCoV Mpro structures: the experimentally resolved structure (PDB 6lu7) in green, Innophore’s homology model (QHD LP1) in orange, and the Zhang Lab’s homology model in blue. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/7d116048-6c65-4eac-8fe7-3fe0597f3adb/image+5.png Blog - 2019-nCov, structurally speaking - part II Figure 5. Overlay of the HIV-1 protease structure (PDB 4l1a) (protein chains colored in orange and purple) and the Innophore LP1 model of the 2019-nCoV protease (in blue) . The overlay is based on the ligand-ligand superposition. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/204db3aa-513e-4ea6-b243-c28f6305d0be/image+6.jpg Blog - 2019-nCov, structurally speaking - part II Figure 6. The drug Baricitinib https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b51873d0-4fc5-401b-8825-13dd9cfc7e43/image+7.png Blog - 2019-nCov, structurally speaking - part II Figure 7. Structure overlay of BMP2K bound to Baricitinib (PDB 4w9x) in green, and AAK1 bound to an inhibitor in blue (PDB 5l4q). Both ligands are bound to the hinge. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/2b1fdeda-0157-433c-8f3d-b35ca2f399f7/image+8.png Blog - 2019-nCov, structurally speaking - part II Figure 8. The 3decision Sequence Viewer. To the left: Sequence alignment of the BMP2K, AAK1 and GAK Mpro sequences. Differences compared to the reference sequence (here: BMP2K) are shown by one-letter codes. Ligand-protein interactions are mapped onto the sequence alignment and colored by type (green=hydrophobic, red=hydrogen bond, purple= water bridge, pink=salt bridge). Each line corresponds to a unique ligand. To the right: Structure overlay of BMP2K bound to Baricitinib (PDB 4w9x) in green, and AAK1 in blue (PDB 5l4q). The BMP2K protein chain, and the AAK1 ligand are hidden. BMP2K’s Ser63 is selected. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/86430c26-c678-4802-b1c5-7f74c0d13ca0/image+9.png Blog - 2019-nCov, structurally speaking - part II Figure 9. A model of an AAK1-Baricitinib complex. https://3decision.discngine.com/blog/2020/02/03/ncov-structurally-speaking monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/bcc11155-09d7-451f-9fae-db33e086b919/coronavirus+replication.png Blog - 2019-nCov, structurally speaking Image credit: Crenim at English Wikipedia, CC BY-SA 3.0 / Wikimedia Commons https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/6685b191-fc42-4073-a99f-c3c4b10bf7be/coronavirus-structure.jpg Blog - 2019-nCov, structurally speaking Image credit: Wikimedia Commons https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/27af03e9-a038-4b19-9b1f-7a30da6dc70c/treatments.png Blog - 2019-nCov, structurally speaking treatments.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/174f6b31-db86-4ef3-82ba-1d8387f57195/3decision+selectivity+analysis.png Blog - 2019-nCov, structurally speaking A selectivity analysis in the 3decision® user interface https://3decision.discngine.com/blog/2020/01/22/whats-new-in-3decision-2020-1 monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/8ab6ea7f-e750-4622-b404-409e56d475e7/ad7d2-tversky.png Blog - What's New in 3decision® 2020.1? Tversky.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/5e14964f-04d0-4333-abbc-35edb0100d84/83b46-bi2536inthe3decisionworkspace.jpg Blog - What's New in 3decision® 2020.1? BI2536 in the 3decision Workspace https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/26fb7362-a6e0-4dac-9f92-f3545a4c1506/7e764-projectreferncestructure.png Blog - What's New in 3decision® 2020.1? Project Refernce Structure https://3decision.discngine.com/blog/2020/01/20/the-growing-mountain-of-protein-structural-data-challenges-and-opportunities-in-structure-based-drug-discovery-sbdd monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/4b90b0da-1957-4188-831a-602dbedabdd0/eef2a-proteine.jpg Blog - Discover 3decision® - Part 1: The Growing Mountain of Protein Structural Data Molecular representation of a ligand-binding-site. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1f11baac-46a7-409f-8b5b-d233647e9bd8/535ac-rcsbpdbstatistics.png Blog - Discover 3decision® - Part 1: The Growing Mountain of Protein Structural Data The overall growth of released PDB structures in the last 30 years. (Source: https://www.rcsb.org) https://3decision.discngine.com/blog/2019/09/04/lundbeck-selects-discngines-3decision-platform-to-leverage-complex-protein-ligand-3d-structure-data-in-the-discovery-of-new-treatments-of-brain-diseases monthly 0.5 2024-11-13 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/12897901-9f42-4f29-86b1-726d139df7bd/e3b5d-sequenceexplorer.png Blog - Lundbeck selects Discngine’s 3decision® platform One of the structural analytics tools in 3decision® - the sequence explorer. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b4b919ba-2e59-4c02-84cb-1944b2c57f43/Discngine+Logo+Dark+Background.png Blog - Lundbeck selects Discngine’s 3decision® platform Discngine-Logo-Couleur-Big-Fond.png https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e9f42670-4eee-48a0-ad82-b71e71fd989c/LUNDBECK%2B3decision.png Blog - Lundbeck selects Discngine’s 3decision® platform LUNDBECK-logo-RGB.jpg https://3decision.discngine.com/blog/2019/06/26/mockuping-using-adobe-xd-for-scientific-web-app-development monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1fcf8855-fbcb-46c9-a587-17bea4e1a7f5/a52d3-screenshotof3decision27ssequenceexplorerlayout.png Blog - Using Adobe XD for Scientific Web app development - do your mockups 3decision’s sequence explorer layout - just as an example https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1709250813065-C30R0LZUMZSUAJZUAUE1/127c4-screenshot2019-06-26at23.32.26.png Blog - Using Adobe XD for Scientific Web app development - do your mockups - Design Mode Design screens, make reusable elements https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1709250832200-KD5CCDI98NFDWPHZ1TU1/e6aa4-screenshot2019-06-26at23.35.11.png Blog - Using Adobe XD for Scientific Web app development - do your mockups - Create workflows Connect screens or elements on different screens to create user workflows https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1709250822842-58LRF9Q1LH32CASB9H0Z/b6c6c-screenshot2019-06-26at23.33.06.png Blog - Using Adobe XD for Scientific Web app development - do your mockups - Share Share with your end-users or with other developers https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1709250839963-BU4PLBBOD1O11HEP1XTT/b66a3-screenshot2019-06-26at23.35.51.png Blog - Using Adobe XD for Scientific Web app development - do your mockups - Simulation mode Quickly simulate your workflow and record screens and voice to a video https://3decision.discngine.com/blog/2019/06/12/openforcefield-040-parametrization-tests-on-xchem-and-rcsb-data monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/6d4683c6-fe19-4386-b132-1edb270c12f0/7c513-screenshot2019-06-13at00.47.33.png Blog - OpenForcefield 0.4.0 parametrization tests on XChem Data Browsing the results in the awesome ligand browser in 3decision ;) - sorry no impartiality here https://3decision.discngine.com/blog/2019/06/06/tethered-minimization-of-small-molecules-with-rdkit-towards-tethered-docking-on-proteins-with-rdock monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/92cbd098-eb5b-4be2-b3dc-973b2142ffd3/c743b-pu8.png Blog - Tethered minimization of small molecules with RDKit PU8 ligand in RCSB PDB structure 1uyd https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/0dd27eae-62ad-4fbb-9a8f-21e58961fe72/34d17-hsp90_mols.png Blog - Tethered minimization of small molecules with RDKit Compounds we’d like to dock https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1a2565c2-7142-42ab-8029-0d5fdf043007/e8c28-screenshot2019-06-06at23.24.32.png Blog - Tethered minimization of small molecules with RDKit Now we have the TETHERED ATOMS in the output SD file - ready for rdock https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/65356f6e-fd1a-4acc-925e-36327bd67594/175f1-3decision_3dviewer_image.png Blog - Tethered minimization of small molecules with RDKit Final aligned and minimized molecules - all adenins are perfectly aligned and even other parts of the molecule are as well, if the MCS was bigger than the adenine fragment. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c24335b0-1ef7-4fd9-9b8a-5a12fcae7125/e8c28-screenshot2019-06-06at23.24.32.png Blog - Tethered minimization of small molecules with RDKit Excerpt from the rdock documentation https://3decision.discngine.com/blog/2019/05/29/webinar2 monthly 0.5 2024-03-01 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/46634eed-b0a4-45b0-9561-1a6273588d68/3decision_webinar2.jpg Blog - Webinar: Discover 3decision, Winner of the Innovative Practices Award at Bio-IT 2019! Peter & Gabriella from the 3decision team https://3decision.discngine.com/blog/2019/05/24/building-the-vmd-molfile-plugin-from-source-code monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/973e8e22-c05c-4957-bf46-9e74cb64ff16/6a07f-finalcompiledmolfileplugin.png Blog - Building the VMD molfile plugin Final compiled molfile plugin https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/500ec23a-cc1c-4a38-90a0-fbd4b0bfa008/28adf-screenshot2019-05-26at22.10.41.png Blog - Building the VMD molfile plugin Screen Shot 2019-05-26 at 22.10.41.png https://3decision.discngine.com/blog/2019/04/24/discngine-and-abbvie-winner-of-the-innovative-practices-award-at-bio-it-2019 monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/926dc42c-16e7-4c50-80ce-c11dbc6bfea8/BIT%2BInnovative%2BPractics-Award-WINNER_small.jpg Blog - Discngine and AbbVie, winners of the Innovative Practices Award at Bio-IT 2019! BIT Innovative Practics-Award-WINNER.jpg https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/2c86aa93-5f84-40d3-9ffd-8e96c578a280/9f7a3-3decision-user-interface.png Blog - Discngine and AbbVie, winners of the Innovative Practices Award at Bio-IT 2019! 9f7a3-3decision-user-interface.png https://3decision.discngine.com/blog/2018/04/26/biomolecular-structures-how-to-maximize-the-value-of-what-you-already-have monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1a2f6751-d829-4eb8-9519-b9428f7bb2a1/Webinar1.jpg Blog - Webinar: Biomolecular structures: How to maximize the value of what you already have Peter & Gabriella from the 3decision team https://3decision.discngine.com/blog/2018/04/09/were-launching-our-very-first-webinar monthly 0.5 2024-05-06 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/8557d312-f3e2-4105-841a-d6602c616c3f/4990e-discngine-3decision-invitationwebinar201804.png Blog - We're launching our very first Webinar! Discngine - 3decision - invitation webinar 201804.png https://3decision.discngine.com/blog/2018/03/29/3decision-20183 monthly 0.5 2024-05-06 https://3decision.discngine.com/blog/2017/05/10/website-launch monthly 0.5 2024-05-06 https://3decision.discngine.com/blog/category/Products monthly 0.5 https://3decision.discngine.com/blog/category/Events monthly 0.5 https://3decision.discngine.com/blog/category/Release+Note monthly 0.5 https://3decision.discngine.com/blog/category/Webinar monthly 0.5 https://3decision.discngine.com/blog/category/ScienceBlog monthly 0.5 https://3decision.discngine.com/blog/category/TechBlog monthly 0.5 https://3decision.discngine.com/blog/category/Press+Release monthly 0.5 https://3decision.discngine.com/blog/category/Uncategorized monthly 0.5 https://3decision.discngine.com/blog/tag/python monthly 0.5 https://3decision.discngine.com/blog/tag/UX monthly 0.5 https://3decision.discngine.com/blog/tag/open+source+software monthly 0.5 https://3decision.discngine.com/blog/tag/molecular+dynamics monthly 0.5 https://3decision.discngine.com/blog/tag/vmd monthly 0.5 https://3decision.discngine.com/blog/tag/rdock monthly 0.5 https://3decision.discngine.com/blog/tag/Design monthly 0.5 https://3decision.discngine.com/blog/tag/docking monthly 0.5 https://3decision.discngine.com/blog/tag/rdkit monthly 0.5 https://3decision.discngine.com/blog/tag/scripting monthly 0.5 https://3decision.discngine.com/blog/tag/UI%2FUX monthly 0.5 https://3decision.discngine.com/blog/tag/UI monthly 0.5 https://3decision.discngine.com/blog/tag/compilation monthly 0.5 https://3decision.discngine.com/blog/tag/install monthly 0.5 https://3decision.discngine.com/blog/tag/minimization monthly 0.5 https://3decision.discngine.com/blog/tag/3decision monthly 0.5 https://3decision.discngine.com/blog/tag/integration monthly 0.5 https://3decision.discngine.com/blog/tag/AdobeXD monthly 0.5 https://3decision.discngine.com/blog/tag/superimpositioning monthly 0.5 https://3decision.discngine.com/blog/tag/alignment monthly 0.5 https://3decision.discngine.com/blog/tag/User+Studio monthly 0.5 https://3decision.discngine.com/protein-of-the-month-collection daily 0.75 2026-03-30 https://3decision.discngine.com/protein-of-the-month-collection/2026/03/31/gipr monthly 0.5 2026-03-30 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1774612138685-IOCPCID93C2NSN80QPKL/GIPR+gallery.png Protein of the Month - GIPR - Make it stand out GIPR https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/5ab0e47c-2efd-4cb5-8f04-85883ff4148f/Image+1.png Protein of the Month - GIPR - Make it stand out Image 1. Cryo-EM structure (PDB code: 8YW4) of GIPR (in light green) in complex with peptide retatrutide (in yellow). The N-terminal of the peptide is buried in the receptor transmembrane domain (TMD), and the C-terminal engages the extracellular domain (ECD). Image is produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/265e923d-bdaa-4182-8892-673aa47f9bc8/Image+2.png Protein of the Month - GIPR - Make it stand out Image 2. Cryo-EM structures of retatrutide in complex with: GIPR (PDB code: 8YW4, receptor in green, peptide in yellow); GCGR (PDB code: 8YW5, receptor in grey, peptide in red); GLP1R (PDB code: 8YW3, receptor in pink, peptide in teal). Structures are aligned on the receptor chain (reference structure: GIPR: retatrutide complex, GIPR chain). The receptors are aligned on the GIPR structure to highlight the similar overall binding arrangement. Overlay and image generated with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/89148b41-75cd-48ad-988e-464fdd3a7014/Image+3.png Protein of the Month - GIPR - Make it stand out Image 3. Focus on the ECL1 region of the retatrutide complexes (GIPR complex, PDB code 8YW4, receptor in green, peptide in yellow; GCGR complex, PDB code 8YW5, receptor in grey, peptide in red; GLP1R, PDB code 8YW3, receptor in pink, peptide in teal). The proline residues in GIPR ECL1 region are in the balls-and-stick representation and labeled. The structures overlay and image are produced with the 3decision® software. https://3decision.discngine.com/protein-of-the-month-collection/2026/02/11/nlrp3 monthly 0.5 2026-02-17 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ceaefd71-7d2e-446c-88e5-638d39ab6a03/8SXN.png Protein of the Month - NLRP3 - Make it stand out NLRP3 https://3decision.discngine.com/protein-of-the-month-collection/2025/12/5/menin monthly 0.5 2026-02-11 https://3decision.discngine.com/protein-of-the-month-collection/2025/11/3/ras monthly 0.5 2025-12-19 https://3decision.discngine.com/protein-of-the-month-collection/2025/6/25/trem2 monthly 0.5 2025-12-19 https://3decision.discngine.com/protein-of-the-month-collection/2025/5/20/brinp2 monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/037bf0ab-7d8b-40b0-8610-ece9e075ce65/3decision_3dviewer_image+%2810%29.png Protein of the Month - BRINP2 - Make it stand out BRINP2 https://3decision.discngine.com/protein-of-the-month-collection/2025/4/23/apelin-receptor monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/0611398c-b10a-44a8-bcd1-ea3031f6873b/protein+image+apelin%281200+x+1200+px%29.png Protein of the Month - APLNR - Make it stand out Apelin receptor https://3decision.discngine.com/protein-of-the-month-collection/2025/3/11/nav-18 monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/a1736973-beff-461b-a4b7-ea5f1a5fa126/nav1.8+%281%29.png Protein of the Month - Nav1.8  - Make it stand out Nav 1.8 https://3decision.discngine.com/protein-of-the-month-collection/2025/2/19/c-x-c-chemokine-receptor-4-cxcr4 monthly 0.5 2025-12-19 https://3decision.discngine.com/protein-of-the-month-collection/2025/1/21/mi-opiod-receptor monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b7dc53c3-23df-4f4b-8e5e-3c3de6dc509c/uOR_gallery+%281%29.png Protein of the Month - µ-Opiod Receptor - Make it stand out µ-Opiod Receptor https://3decision.discngine.com/protein-of-the-month-collection/2024/12/4/lps-transporter monthly 0.5 2025-12-02 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/afa99604-b6fb-43ec-a591-a0e98c2f9cc2/Cryo-EM+high-resolution+structure+of+the+A.+baylyi+Lpt+complex+%28LptB2FG%2C+PDB%3A+8FRL. Protein of the Month - LPS transporter (Lpt)  - Make it stand out Image 1. A) Macrocyclic peptide compound 1. At the top , the 3D structure of the compound in the binding site (PDB: 8FRL). At the bottom is the 2D chemical structure of the molecule. B) Cryo-EM high-resolution structure of the A. baylyi Lpt complex (LptB2FG, PDB: 8FRL. LptF is in pink, LptG in grey) bound to LPS (in yellow) and compound 1 (in light blue). The interaction network between the drug, the Lpt residues, and the native ligand LPS are represented as dotted lines, color-coded in light blue for aromatic and yellow for polar contacts. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ca98ffc3-176a-47ef-9a29-bd7d5cfe0014/Image2.png Protein of the Month - LPS transporter (Lpt)  - Make it stand out Image 2. Overlay of the LPS binding site of complex Lpt:LPS:1 (PDB: 8FRL; LptF in pink, LPS in yellow, compound 1 in light blue) to the complex Lpt:LPS (PDB: 8FRM; LptF in blue, LPS in light green). Notice that the LPS conformation in both complexes is almost identical, indicating that the interaction with compound 1 does not alter LPS binding. The drug seems to trap an LPS-bound state of the Lpt complex. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/8cf3f77c-4ec8-4ba0-9d61-c5fc213ae61c/Image3.png Protein of the Month - LPS transporter (Lpt)  - Make it stand out Image 3. Comparison of the LPS binding site for the complex Lpt containing the LptC protein (LptB2FGC; PDB: 8FRP; LptFG in light orange, LptC in red) and without LptC (LptB2FG:LPS:1 complex; PDB: 8FRL; LptF in pink, LptG in grey, LPS in yellow, compound 1 in light blue). Notice that the LptC helix occupies the same region of one of compound 1 substituents. This is an indication that the “closed” conformation of the LptC helix would prevent drug binding, and that compound 1. https://3decision.discngine.com/protein-of-the-month-collection/2024/10/16/mc4r monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/d30f4afc-b284-4685-983d-4f99683f3d0e/MC4R+nanobody+pN162+complex.png Protein of the Month - MC4R  - Make it stand out Image 1. 3D structure of the MC4R complex with nanobody pN162 (PDB: 8QJ2). MC4R is colored in light orange, pN162 in white, ConfoBody Cb35 in light green, and Gαs, Gβ, and Gγ in purple, red, and grey, respectively. The panel zooms in on the orthosteric pocket and pN162 CDR3 binding. The binding pose of the endogenous agonist α-MSH is represented in red and is obtained by overlay of the MC4R:α-MSH complex structure (PDB: 7F53; the cartoon representation of MC4R is omitted for clarity). The pictures were produced using the 3decision® software and its Annotation browser feature. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e434e832-d43e-4cf7-b2a5-28c48de0413e/Comparison+between+active+and+inactive+MC4R.png Protein of the Month - MC4R  - Make it stand out Image 2. Comparison between active and inactive MC4R. A) Overlay of MC4R complexes with nanobody pN162 (PDB: 8QJ2, white), α-MSH (PDB: 7F53, pink), and setmelanotide (PDB: 7PIU, blue). In all three structures it is shown how the binders stabilize the active form of the receptor. B) Overlay of MC4R complexes with nanobody pN162 (PDB: 8QJ2, white), and the antagonist SHU9119 (PDB: 6W25, orange). The antagonist SHU9119 stabilizes the receptor in an inactive conformation, as indicated by the position of TM6 in the inward conformation, which is highlighted in the light blue circle. The pictures were produced using the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b9e376b6-03ba-4640-b7ac-85e7be6f597f/Image3.png Protein of the Month - MC4R  - Make it stand out Image 3. Analysis of the binding modes of agonist ligands to MC4R. Dashed lines represent the interaction networks: polar interactions are in yellow, hydrogen bonds in blue, and metal-mediated interactions in purple. A) Setmelanotide interaction with MC4R (PDB: 7PIU, MC4R in yellow, setmelanotide in pink, Ca2+ ion in light grey) shows calcium ion coordination of MC4RGlu100 and MC4RAsp126 residues (labeled in yellow). B) pN162 binding with MC4R (PDB: 8QJ2, MC4R in orange, pN162 in green) does not require the presence of Ca2+: the pN162Arg101 residue forms salt bridges with the residues MC4RGlu100 and MC4RAsp126 instead of the calcium coordination. The pictures were produced with the 3decision® software. https://3decision.discngine.com/protein-of-the-month-collection/2024/9/30/nmdar monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/facfd88c-e139-407d-83e5-ae94cae91810/NMDAR-Fab+complex.png Protein of the Month - NMDAR - Make it stand out Image 1. 3D structures of NMDAR-Fab complexes with distinct epitope binding: Fab2G7 interacts with the top, while Fab5F6 with the side of NMDAR N-terminal domain. A) NMDAR-Fab2G7 complex (PDB: 8JJ2; Fab2GT in blue, NMDAR is colored by chain: GluN1 in green and purple, GluN2 in orange and red). The NTD domain and its R1 lobe are indicated by green labels, the binding region is highlighted in the blue circle. B) NMDAR-Fab5F6 complex (PDB: 8JJ0; Fab5F6 in white, NMDAR is colored by chain: GluN1 in green and purple, GluN2 in orange and red). The NTD domain and its R1 lobe are indicated by green labels, the binding region is highlighted in the white circle. C) Overlay of the NMDAR-Fab2G7 complex (PDB: 8JJ2, blue) and NMDAR-Fab5F6 complex (PDB: 8JJ0, white). The pictures are produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/6e5dace7-64a0-4873-99f2-e2808cd7cdbe/Protein-protein+interactions+NMDA+receptor-FAB+complexes.png Protein of the Month - NMDAR - Make it stand out Image 2. Analysis of the PPIs of NMDAR-Fab complexes and different interaction pattern. A) Interface between GluN1-NTD and Fab5F6 (PDB:8JIZ; Fab5F6 in white, GluN1 in green). The GluN1 residues Arg36 and Lys37 are labeled in green. B) Interface between GluN1-NTD and Fab2G7 (PDB:8JJ1; Fab2G7 in blue, GluN1 in green). Dashed lines represent the PPIs network: polar interactions are in yellow, hydrogen bonds in blue, cation-pi interactions in red. The GluN1 residues Gln48 and Lys51 are labeled green.). The pictures are produced with the 3decision® software. https://3decision.discngine.com/protein-of-the-month-collection/2024/8/23/her2 monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/f92e4497-e8a6-4c96-b2ae-18962adabd73/HER2+ternary+complex+with+trastuzumab+and+trus+pertuzumab+%28HTP%29+cryoEM.png Protein of the Month - HER2 - Make it stand out Image 1. HTP overall complex (PDB: 8PWH). HER2 is colored by domains (blue: I; grey: II; orange: III; cyan: IV), the pertuzumab Fab is colored in green and dark red, and the trastuzumab Fab in purple and orange. The domains of HER2 are highlighted using the 3decision® Annotation Browser. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/4a6b57db-3fd5-49cf-94a1-1da081d60ee0/Superposition+of+HER2+ternary+complex+with+trastuzumab+and+trus+pertuzumab+%28HTP%29+X-ray+and+cryoEM.png Protein of the Month - HER2 - Make it stand out Image 2. Comparison of the cryo-EM HTP complex (PDB: 8PWH; HER2 in brown, pertuzumab variable light chain VL in red, pertuzumab variable heavy chain in green VH) with the HER2-pertuzumab crystal structure (PDB: 1S78; white). The antibody-antigen interactions on the cryo-EM solved structure are shown (calculated with the 3decision® protein-protein interactions tool). Residue side chains are represented as lines. The picture is produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e71034c3-b4c9-4883-99fd-885035c17194/CryoEM+HER2-trastuzumab+interface+analysis.png Protein of the Month - HER2 - Make it stand out Image 3. HER2-trastuzumab interface analysis. A) The new cryo-EM HTP complex focused on the HER/terstuzumab interface (PDB: 8PWH). HER2 IV domain in cyan, trastuzumab variable heavy chain in purple with CDR3 highlighted in green. The electron density map is shown as a white mesh with a contour level set to 11. The yellow arrow points to the map, highlighting the interaction between the residue R98 of trastuzumab and the IV domain loop residue D585. The antibody-antigen interactions are shown with the 3decision® protein-protein interactions tool. B) A previous cryo-EM HTP complex structure focused on the HER/terstuzumab interface (PDB: 6OGE). HER2 IV domain in cyan, trastuzumab variable heavy chain in brown with CDR3 highlighted in green. The electron density map is a white mesh with a contour level set to 11. No electron density map is observed between the R98 and the IV loop residues (highlighted in white). https://3decision.discngine.com/protein-of-the-month-collection/2024/7/29/pd-1 monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/353bc164-957b-4cd3-b8b0-732a141a8e05/PD-1cemiplimab+complex%2C+PDB+7WVM.png Protein of the Month - PD-1 - Make it stand out Image 1. A) 3D structure of the PD-1/cemiplimab complex (PDB: 7WVM; PD-1 in pink, cemiplimab heavy variable chain (VH) in red, light variable chain (VL) in green). BC and FG loops on PD-1 are indicated by the pink arrows. Protein-protein interactions (PPIs) between cemiplimab and PD-1 are indicated as dashed lines and calculated with the software 3decision®. B) Overlay of the PD-1/cemiplimab complex (PDB: 7WVM; PD-1 in pink, cemiplimab heavy variable chain (VH) in red, light variable chain (VL) in green) and of the PD-1/PD-L1 complex structure (PDB: 4ZQK; PD-1 in yellow, PD-L1 in white). Superposition by chain is performed using the PD-1 chain as a reference for the alignment. BC and FG loops on PD-1 are indicated by the pink arrows as a reference. All pictures are produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/f6e0376f-48de-4a16-91d7-60ff81c42395/Superposition+of+PD-1+binding+to+various+therapeutic+antibodies.png Protein of the Month - PD-1 - Make it stand out Image 2. Overlap of the 3D structure of PD-1/cemiplimab complex (PDB: 7WVM, pink) with the PD-1 complex with the following mABs: A) camrelizumab (PDB: 7CU5, orange) and MW11-H317 (PDB: 6JJP, white); B) pembrolizumab (PDB: 5JXE, green) and nivolumab (PDB: 5WT9, cyan). Superposition is performed using the PD-1 chain as a reference for the alignment. Pictures are produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/7b447041-fef1-4eb3-9a9c-12384b10d47d/Superposition+of+the+3D+structure+of+PD-1-cemiplimab+complex+with+the+PD-1-camrelizumab+complex.png Protein of the Month - PD-1 - Make it stand out Image 3. Overlap of the 3D structure of PD-1/cemiplimab complex (PDB: 7WVM, pink) with the PD-1/camrelizumab complex (PDB: 7CU5, white, glycan chain is green). Superposition is performed using the PD-1 BC loop as a reference for the alignment. The BC loop and Asn58 locations on PD-1 are indicated with a yellow arrow, the position of the HCDR2 on the mAbs is indicated with a light blue arrow. Picture produced with the 3decision® software. https://3decision.discngine.com/protein-of-the-month-collection/2024/6/19/ccr8 monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/8853b14d-dcb7-4dcb-86bb-eab593fb5eb3/Image1.png Protein of the Month - CCR8 - Make it stand out Image 1. Cryo-EM model of the Fab1-CCR8 complex (PDB: 8TLM; CCR8 in red, Fab1 heavy variable chain (VH) in orange, Fab1 light variable chain (VL) in purple). ELC1 is highlighted in green, and ECL2 is highlighted in cyan, using the 3decision® Annotation Browser feature. The location of the N-terminus and ECL3 are indicated by the light grey arrows. Zoomed-in panels show details of protein-protein interactions (PPIs) between the ECL2 and the CDRH3 (a) and CDRH1 (b). PPIs are calculated by the software 3decision®. Measurement distances between the ECL2 and CDRH3 β-strands are reported (a). In the bottom-right box the protein is rotated to show the PPIs between the CDRH1 and ECL2. All pictures are produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/a387946b-d614-420f-a12c-b7b39436a0f1/Image2.png Protein of the Month - CCR8 - Make it stand out Image 2. 3D structure of the complex between 5-HT2B and an antibody Fab fragment (PDB: 5TUD; 5-HT2B in green, Fab light chain in dark red, Fab heavy chain in pink). ELC2 is highlighted in orange, using the 3decision® Annotation Browser feature. The CDRH3 is indicated by the arrow. PPIs between the ECL2 and the CDRH3 are represented. PPIs are calculated by the software 3decision®. https://3decision.discngine.com/protein-of-the-month-collection/2024/5/27/wrn monthly 0.5 2025-12-02 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ed8ef232-c672-44dd-9a2c-405e6fb03bed/Image+1.png Protein of the Month - WRN - Make it stand out Image 1. A) The WRN helicase complex with HRO761 (PDB: 8PFO, protein in grey and ligand in orange). B) The WRN complex with ATPγS (PDB: 8PFP, protein in pink and ligand in blue). Protein domains are highlighted using the 3decision® Annotation Browser function and colored as follows: D1 in green, D2 in blue, and the zinc-binding domain in yellow. The ligand surfaces, produced with the 3decision® software, are in orange for HRO761 and blue for ATPγS. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/a6a84b35-c79e-42f2-a92c-dcc84c947345/Image+2.png Protein of the Month - WRN - Make it stand out Image 2. Overlay of the WRN helicase in complex with HRO761 (PDB: 8PFO, protein in grey and ligand in orange) and ATPγS (PDB: 8PFP, protein in pink and ligand in blue). A) The residues composing the flexible hinge are indicated and the labels are in grey for the HRO761-bound structure and in pink for the ATPγS-bound one: Thr728, Gly729, Phe730, Asp731, Arg732. The picture is produced using the 3decision® highlight mode: the residues with an RMSD higher than 1.4 are displayed as lines and cartoons, while for the residues with a lower RMSD, only the backbone line is represented. This visualization mode allows easy spotting of the conformational change of the flexible hinge induced by the allosteric inhibitor HRO761. B) The Walker motif and Lys577 are highlighted and colored in orange for the HRO761-structure and in blue for the ATPγS-bound one. The Walker motif annotation was highlighted using the 3decision® Annotation Browser. https://3decision.discngine.com/protein-of-the-month-collection/2024/4/24/pf20s monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c88c7455-bb25-44bd-a332-6d4e5877dc8e/Image+1.png Protein of the Month - Pf20S - Make it stand out Image 1. TDI-8304 binding mode with Pf20S. A) Cryo-EM structure of Pf20S in complex with six TDI-8304 molecules (PDB: 8G6E). Pf20S cartoon representation in yellow and molecular surface in grey, ligand molecular surface in magenta. The subunits composing the protein complex are indicated. Surfaces are produced with the 3decision® software. B) Zoom on the TDI-8304 binding site in the β5 subunit. TDI-8304 in pink, β5 subunit residues in blue and the pocket surface is represented in white mesh. Pyrrolidone moiety on TDI-8304 and the residue Ser154 are indicated; hydrogen bonds between pyrrolidone and Ser154 are in the dotted circle. C) Zoom on the TDI-8304 binding site in the β2 subunit. TDI-8304 in pink, β2 subunit residues in mutton red, and the pocket surface is represented in white mesh. Pyrrolidone moiety on TDI-8304 is indicated. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/59dfd962-e3f9-4b91-90e5-0e633493467c/Image2.png Protein of the Month - Pf20S - Make it stand out Image 2. Comparison of the structures of wild-type Pf20S with TDI-8403 (PDB: 8G6E; Pf20S in light grey, TDI-8304 in pink), and Pf20S β6A117D mutant (PDB: 8G6F; in blue). In the dotted grey circle are highlighted the residues at the 117 position: Ala117 in the wild-type (label in light grey), and Asp117 in the mutant (label in blue). The picture is produced using the 3decision® highlight mode: the residues with an RMSD higher than 2 are displayed as lines and cartoons, while for the residues with a lower RMSD, only the backbone line is represented. This visualization mode allows easy spotting of the conformational change induced by the point mutation β6A117D. The region Gly156-Ala161 is flipped in the mutant compared to the wild-type. All pictures are produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/991b7c49-fb62-44e3-8acb-f70ad6cb2cf7/Image3.png Protein of the Month - Pf20S - Make it stand out Image 3. A) Superposition of the TDI-8304 binding pose in the wild-type Pf20S (PDB: 8G6E; Pf20S in light grey, TDI-8304 in pink) with the Pf20S β6A117D mutant (PDB: 8G6F; Pf20S in blue). Residues Tyr158 and Ser154 are labeled in light grey for wild-type and in blue for mutant. The morpholine and pyrrolidinone moieties are indicated. The distance between the pyrrolidinone and the Ser154 NH backbone position in wild-type is 3.11 Å allowing a hydrogen bond, while the Ser154 in the mutant is 4.25 Å. The picture and measurements are produced using the 3decision® software. B) Pf20S β6A117D mutant β5 subunit pocket in complex with WLW-vs (PDB: 8G6E; Pf20S in blue, WLW-vs in green). Residues Tyr158 and Ser154 are labeled; the indole moiety is indicated. The pictures are produced with the 3decision® software. https://3decision.discngine.com/protein-of-the-month-collection/pi3k monthly 0.5 2024-04-02 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/554c306a-b640-4495-a85c-eb38dcc12f5b/Image1.png Protein of the Month - PI3Kα - Make it stand out Image 1: Cryo-EM structure of the H1047R mutant (PDB: 8GUB), with the H1047R residue highlighted and labeled in grey. The p110α subunit is in orange, the p85α subunit in purple. The picture is produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/42eac3e3-9e0f-4197-b126-deea524526ff/Image2.png Protein of the Month - PI3Kα - Make it stand out Image 2: Comparison of X-ray structures of WT p110α (PDB: 8TS7, orange) and H1047R p110α mutant (PDB: 8TS8, blue). A. Highlighted in white are the WT p110α conformations of residues: W1051, H1047, F594, and D915. B. Highlighted in white are the H1047R p110α mutant conformations of residues: R1047, F594, and D915. C. Superposition of the WT and H1047R p110α subunits, represented with the 3decision® highlight mode: the residues with an RMSD higher than 1.5 are displayed as lines and cartoon, while for the residues with a lower RMSD, only the backbone line is represented. This visualization mode allows easy spotting of the conformational differences between the residues composing the allosteric network between mutant and WT. All pictures are produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/d651edb2-3897-4b49-9c9f-9cf500180bd1/Image3.png Protein of the Month - PI3Kα - Make it stand out Image 3: Structures of the H1047R p110α mutant in complex with the novel allosteric inhibitors. 2D chemical structures of compound 2 and RLY-2608 are reported on the right. A. H1047R p110α complex with compound 2 (PDB: 8TSA, protein in white, ligand in grey). The electron density map of the X-ray structure is reported and shows a clear density, indicating the binding site and ligand pose of compound 2. B. Comparison of the binding poses of compound 2 (PDB: 8TSA, grey) and RLY-2608 (PDB: 8TSD, green). The pocket residues and surface of H1047R p110α are reported. The pictures are produced with the 3decision® software. https://3decision.discngine.com/protein-of-the-month-collection/2024/2/20/cftr monthly 0.5 2025-12-02 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/784baded-bb94-4b4f-90c7-f2f584c903c0/new+pic.png Protein of the Month - CFTR - Make it stand out CFTR https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/2872f65e-0ef9-4521-8e97-ec1e6b71977f/Image1.png Protein of the Month - CFTR - Make it stand out Image 1. 3D structure of Δ508 CFTR mutant (in white, PDB: 8EIQ) in complex with the modulators composing Trikafta: ivacaftor (in pink), elexacaftor (in yellow), and tezacaftor (in light blue). In the zoomed-in view are the binding sites for each modulator. The molecular surface of the protein is represented in white, and the electron densities around the ligands are shown as a green mesh. The pictures are produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e836ce0f-ce60-4ce4-91fa-e6083b3827e7/Image2.png Protein of the Month - CFTR - Make it stand out Image 2. Comparison of 3D structures of the Trikafta:Δ508 CFTR complex (in white, PDB: 8EIQ) and the wild-type CFTR (in blue, PDB: 6MSM). A) Overlay of the full structures. Superposition done with the 3decision® software. B) Zoomed-in view on the Phe508 position. TM11 is on the left side (as indicated), and NBD1 is on the right side (grey, dotted circle). The residues Arg1070 (from the mutant Δ508 in white, from the wild-type in blue) and Phe508 (only from the wild-type, since it is not present in the mutant Δ508) are labeled. The electron density of the Trikafta:Δ508 CFTR complex is represented as a green mesh. The pictures are produced with the 3decision® software. https://3decision.discngine.com/protein-of-the-month-collection/2024/1/31/or5k1 monthly 0.5 2024-06-24 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/f9118598-106c-44c8-aa1f-0bdcf1940e4e/Image+1.png Protein of the Month - OR5K1 - Make it stand out Image 1. AF2 model of OR5K1 colored by pLDDT confidence score (on the right, legend of the pLDDT score in terms of confidence of the predicted structure). The picture of the AF model is produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/5b8740b4-afe7-4589-8764-7d45651af5c8/Image+2.png Protein of the Month - OR5K1 - Make it stand out Image 2. Comparison of the OR5K1 AF2-predicted model of ECL2 (colored by confidence score pLDDT) and the experimentally determined structure of ECL2 of the receptor OR51E2 (in pink, PDB: 8F76). The superposition and the picture are produced with the 3decision® software. https://3decision.discngine.com/protein-of-the-month-collection/2023/11/29/serotonin-receptors-5-ht-receptors monthly 0.5 2024-11-14 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/f9a40b9d-b11c-49c6-ad79-5a424dfcd73e/Image+1.png Protein of the Month - Serotonin receptors (5-HT receptors) Image 1. 3D structure of the binding site of serotonin receptors, with representation of three distinct ligand-binding subpockets: A) 5-HT4 in complex with serotonin (PDB: 7XTA; protein in yellow, ligand in purple), in red are highlighted the residues composing the lower orthosteric subpocket; B) same structure as A, in red are the residues composing the upper orthosteric subpocket; C) 5-HT2C in complex with ergotamine (PDB: 6BQG; protein in white, ligand in orange), in red the extended (extracellular-facing) subpocket. Images created and receptor-ligand contacts calculated with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/0fd9fc76-e898-404d-9b96-c4585e07f90e/Image+2.png Protein of the Month - Serotonin receptors (5-HT receptors) Image 2. Overlap of the ligand-binding pocket for complexes of the receptors: 5-HT4 (PDB: 7xta, blue), 5-HT1E (PDB: 7e33, white), 5-HT6 (PDB: 7ys6, green), 5-HT5A (PDB: 7um5, pink) and 5-HT2C (PDB: 8dpf, orange). Ligands are hidden for a clearer view. The picture is produced using the 3decision® highlight mode, which only shows the different residues of the superposed proteins. It can be easily seen that the number of residues shown is higher in the lower orthosteric subpocket (in the green circle) due to the higher diversity with respect to the extended subpocket (in the red circle). https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/4b4a97ef-4ec6-4e2d-80fc-6f16e9b9cad3/Image+3.png Protein of the Month - Serotonin receptors (5-HT receptors) Image 3. Selectivity hotspots in the upper orthosteric pocket between receptors 5-HT2C (PDB: 6BQG, in pink) and 5-HT1B (PDB: 7C61, in grey). 5-HT2C shows a higher hydrophobic character of this pocket (Ile 4x56, Phe 5x39, Val 5x40) compared to the residues at the corresponding position in 5-HT1B (Val 4x56, Tyr 5x39, Thr 5x40). The picture is produced using the 3decision® highlight mode. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/a7e19b4e-bbc1-4c0e-831b-0ff2b3370875/Pockets.png Protein of the Month - Serotonin receptors (5-HT receptors) https://3decision.discngine.com/protein-of-the-month-collection/2023/10/27/cyclin-k monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/275d45c2-c2ed-461a-836f-e9012937149b/Image1.png Protein of the Month - Cyclin K Image 1. Crystal structure of the DDB1-CR8-CDK12-cyclin K complex: cyclin K in aquamarine, CDK12 in yellow, DDB1 in grey, and ligand CR8 in pink (PDB: 6TD3). In the zoomed panel, focus on the binding mode of CR8 at the interface between CDK12 and DDB1, with the phenylpyridine moiety interacting with the Arg928 on DDB1. The purine scaffold of CR8 occupies the ATP binding pocket and interacts with the hinge region. Pictures produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e35313bb-5567-44da-aafd-cd825d20b8db/Image%2B2.png Protein of the Month - Cyclin K Image 2. A) Chemical structure of CR8. In yellow is highlighted the purine scaffold, in red the gluing moiety (the phenylpyridine substituent). B) Overlay of the crystal structures of the DDB1-ligand-CDK12-cyclin K complex, where ligand is respectively: CR8 in pink (PDB: 6TD3), roscovitine in blue (PDB: 8BU9), DS06 in white (PDB: 8BUJ), DS08 in orange (PDB: 8BUK), DS11 in green (PDB: 8BUL). For clarity, the cartoon representation is not displayed. On the right, the chemical structure of the gluing moiety for each of the compounds. Pictures produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/a01b6306-9ad5-47a7-bc28-057b61c0e9e5/Image%2B3.png Protein of the Month - Cyclin K Image 3. A) Overlay of the crystal structures of the DDB1-ligand-CDK12-cyclin K complex, where ligand is respectively: CR8 in pink (PDB: 6TD3), SR-4835 in blue (PDB: 8BU5), 21195 in white (PDB: 8BU7), 919278 in orange (PDB: 8BUA). On the right, the chemical structures of each of the compounds; the gluing moiety is highlighted in red. The picture is produced using the 3decision® highlight mode, which only shows the different portions of the superposed proteins to easily spot the differences among the binding sites. B) Common chemical motifs for cyclin K molecular glue degraders. In green is highlighted the acceptor-donor motif interacting with the CDK12 hinge region; in red is the aromatic gluing moiety, bound to the hydrogen bond donor. https://3decision.discngine.com/protein-of-the-month-collection/2023/9/25/hspb1 monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e66dbdb9-f1fe-4668-9a50-6097fb5de433/picture+1.jpg Protein of the Month - HSPB1 Image 1: A) Brivudine 2D chemical structure, B) 3D structure of the Brivudine-kinase complex (PDB: 2VQS). The interactions selected as a starting point for the search are aromatic interaction between nucleobase of BVDU and the phenylalanine and halogen bond between bromovinyl moiety and serine (interactions are indicated with blue arrows). https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/3cadb2df-7915-45bf-90ca-71c883f196ee/Picture2.jpg Protein of the Month - HSPB1 Image 2: A) Amodiaquine 2D chemical structure; B) comparison of the binding mode of Brivudine and Amodiaquine. The interaction pattern including both the halogen and aromatic bond observed in the brivudine-kinase complex (PDB: 2VQS) are present in the amodiaquine-HNMT structure (PDB: 2AOU) (interactions are indicated with blue arrows). The superposition was done with the 3decision software. https://3decision.discngine.com/protein-of-the-month-collection/2023/8/8/hiv1-ca monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/6e541008-0657-43b4-9271-f7bd78f43fda/3dec-Image+1A.png Protein of the Month - HIV-1 CA https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/76a2a09a-a076-4239-93d7-8bc2cb197f67/3dec-Image+1B.png Protein of the Month - HIV-1 CA - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/f0670bff-0b15-4ad1-b194-c94dd568260e/3dec-Image+2.png Protein of the Month - HIV-1 CA Image 2. Overlay of HIV-1 CA in complex with: lenacapavir (ligand in pink, protein in dark orange, PDB: 6V2F), NUP153 (in white, 4U0D) and CPSF6 (in blue, 4U0B). The picture is produced using the highlight mode of 3decision® software, which only shows different parts of the compared proteins. The orange helix is from the structure in the complex with lenacapavir, which is shifted in position compared to the helixes of the structures in complex with the co-factors. https://3decision.discngine.com/protein-of-the-month-collection/2023/7/11/mcl1 monthly 0.5 2024-03-28 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/af260a54-9b83-418f-a05c-eebe2be3791a/Picture1A.png Protein of the Month - Mcl1 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ccf759d9-2628-4c3e-8526-9f39518907e6/Picture1B.png Protein of the Month - Mcl1 - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/087afa73-8c27-4a4b-8c09-300a0fb494c7/Picture2.png Protein of the Month - Mcl1 Image 2. BH3 binding domain of MCL-1 (in white, PDB: 6YBL) in complex with known inhibitors: S64315/MIK665 (in orange, PDB: 6YBL), AZD5991 (in brow, PDB: 6FS0) and AM-8621 (in blue, PDB: 6OQC). The Arg263 residue and the different sub-pockets (P1-P4) in the binding site are indicated. The protein-ligand interactions and the molecular surface of the pocket (colored by hydrophobicity) were calculated by the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c10df82d-16e3-4ac1-b4a6-0dd8c9f8ad1a/Picture3A.png Protein of the Month - Mcl1 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/eb16af76-8c97-4f21-9964-4648a9c035bc/Picture3B.png Protein of the Month - Mcl1 - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/811a24da-1c71-49cc-a3d8-d5237db5dd14/Picture4.png Protein of the Month - Mcl1 Image 4. Superposition of Mcl-1 in complex with ligand 12 (in brick red, PDB: 8G3T) and compound 28 (in white, PDB: 8G3W). Waters that have been displayed by the expansion of the ligand are indicated by the red arrows. The interactions that the compound 28 form with Thr266 and Gly262 are indicated by the white arrows. Protein-ligand interactions are automatically calculated by the 3decision® software. https://3decision.discngine.com/protein-of-the-month-collection/2023/6/8/er monthly 0.5 2024-03-28 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ba5e70ee-4edc-412f-9f4a-0a0e641e77d3/Picute+0.png Protein of the Month - ERα https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/86ed0ccf-000b-4336-b795-828e8a854363/Picture1.png Protein of the Month - ERα Image 1. Comparison of ERα in complex with an estrogen (orange, PDB: 1GWR), a SERD (white, PDB: 7R62) and a SERM (blue, PDB: 5W9C). A: Superposition of the complexes with an indication of LBD, H12, and AF-2 positions. The 3decision® highlight mode only shows the different portions of the superposed protein. In this way, it is easy to spot the big conformational change of the H12 helix induced by SERD and SERM binding, which moves from the top of LBD and occupies the AF-2 cleft. B: Comparison of the binding of the estrogen, SERD, and SERM molecules: the cores of the three ligands bind very similarly in the LBD, but the side arms on the SERD and SERM protrude towards the H12, inducing its conformational change. The pictures are produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b8bd7904-1751-4068-bc42-fbdddaf09636/Picture2.png Protein of the Month - ERα Image 2. Overlay of ERα in complex with elacestrant (pink, PDB: 7TE7) and the SERM lasofoxifene (green, PDB: 6VJD). For clarity, the cartoon are hidden and only pocket residues are shown. Indications of H3, H8, H11 and H12 are reported, and the pocket surface is represented. Elacestrant adopts an “L-shaped” orientation and its D ring protrudes towards H8. Lasofoxifene binds with a classical T-shaped orientation. The ligand-protein interactions are automatically calculated by 3decision®. The picture is produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/aaf544bc-1bc3-4049-b458-c862b63147be/Picture3.png Protein of the Month - ERα Image 3. On the left: 2D chemical structure of the newly developed compound TI6-29. On the right: overlay of Erα in complex with elacestrant (pink, PDB: 7TE7), laso (green, PDB: 6VJD), and the newly developed TI6-29 (white, PDB: 8DVB). H3, H8, H11, and H12 are indicated. Only pocket residues and protein-ligand interactions from T6I-29 are shown for clarity. The ring D of the compound adopts a unique position towards H8, and the side arm protrudes towards the loop connecting H11-H12. Superposition of structures is done with the 3decision® software. https://3decision.discngine.com/protein-of-the-month-collection/2023/5/3/blc6 monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/bb045601-bffd-41a0-b94d-6a5f0d8de250/Image1.png Protein of the Month - BLC6 Image 1. 3D structure of BCL6 bound to inhibitor 2 (blue, PDB: 7OKH). The hydrophobic pocket close to position-3 in the ligand is indicated. The molecular surface of the pocket is colored by hydrophobicity index, with green indicating high hydrophobicity. The picture is produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/5be9a346-b126-4e03-8eff-dc6991dba390/Image2.png Protein of the Month - BLC6 Image 2. On the left: overlay of the ligand poses. Ligand 7 (purple, PDB: 7Q7T) sits on top of the pocket, with the lactone oxygen (pointed by the blue arrow) away from the molecular surface of BCL6 (mesh, hydrophobicity index colored), while ligand 9a (white, PDB: 7Q7U) adopts a conformation that fills the space of the pocket. On the right: 2D structures of ligands 7 and 9a, with indication of the lactone oxygen. The picture is produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/9d5225db-8e3c-48c5-a784-c4a7c85283a6/Image3.png Protein of the Month - BLC6 Image 3. Substitution with a cyclopropyl two fluorine atoms (PDB: 7Q7R) increase the shape complementarity of ligand-protein surface. The molecular surfaces of BCL6 (solid, light purple) and of ligand 1 were calculated by the 3decision® software. https://3decision.discngine.com/protein-of-the-month-collection/2023/3/30/pld monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/deb1516c-c54f-468a-9380-f734291a790b/Image1.png Protein of the Month - PLD Image 1. On the left: 2D structures of known hPLD inhibitors – inhibitor 3 and inhibitor 4. On the right: interaction network of the 3D structure of inhibitor 3 (in light pink) in the hPLD2 catalytic site (orange, PDB: 6OHS). The residues composing the binding site are represented as orange sticks, and the surface of the pocket is in a mesh. The protein-ligand interactions are automatically computed by the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/46b40591-6d83-4dd9-9772-28f9fc9a6d37/Image2.png Protein of the Month - PLD Image 2. On the left: 2D structure of the newly discovered inhibitor 5. On the right: comparison of the binding mode of inhibitor 3 (light pink, PDB: 6OHS) and inhibitor 5 blue, PDB: 6OHR). The B-ring of inhibitor 5 projects into a deep pocket next to the A-ring (on the right) and forms additional contacts with the protein. For clarity, the protein representation of complex with inhibitor 3 is omitted, but the surface of the pocket is depicted, color-coded by hydrophobicity index. Also, for the complex with inhibitor 5, only the residues composing the binding site are represented as blue sticks. The protein-ligand interactions are automatically computed by the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/dae14e60-6642-446f-9d03-c39ddaa90f33/Image3.png Protein of the Month - PLD Image 3. Comparison of the binding sites of hPLD2 (in orange, PDB: 6OHS) and hPLD1 (in blue, PDB: 6OHR). The binding poses of inhibitors 3 and 4 are shown (green, PDB: 6OHQ). The methyl on inhibitor 4 gets very close to the L514 compared with F614, which disfavors the binding of this ligand. Inhibitor 3, instead, allocates the methyl in a different region of the binding site and is not affected by the presence of the bulky leucine.The molecular surface of the hPLD2 binding site is depicted for clarity (orange). The picture is produced with the highlight mode of 3decision® software, which only shows the differences among residues in the binding site. This allows to easily identify sequence differences among the compared proteins. https://3decision.discngine.com/protein-of-the-month-collection/2023/3/15/b-catenin monthly 0.5 2025-12-19 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c40a221a-77a6-4ae6-b299-125a593cd0d8/3decision_3dviewer_image+%2871%29.png Protein of the Month - β-catenin Image 1. 3D structure of β-catenin interacting with the α-helical portion of two regulatory proteins: Axin (purple; PDB: 1QZ7) and TCF4 (blue; PDB: 1JDH). The picture is produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ce09c738-0cbb-45a3-bc70-f4667127b871/PPI+catenin+FP015671.png Protein of the Month - β-catenin https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/d1c0a21e-e588-4ee4-add5-5ff06b723a3e/PPI+catenin+Axin1.png Protein of the Month - β-catenin Protein-protein interactions network between β-catenin and Axin PDB: 1QZ7 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/9a4d1788-7563-4b93-ba3a-80b4901a7544/3decision_3dviewer_image+%2872%29.png Protein of the Month - β-catenin Image 3. Superposition of 3D structures of β-catenin in complex with Helicon FP05874 (yellow; PDB:7uwo), Axin (purple; PDB: 1QZ7) and TCF4 (blue; PDB: 1JDH) to locate the difference in the binding site. For simplicity, the chain of the β-catenin is not displayed for Axin and TCF4. The figure is produced with the 3decision® software. https://3decision.discngine.com/protein-of-the-month-collection/2023/2/7/sglt2 monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1d103d23-1719-4d08-b280-2ce143bd2816/Image1-empagliflozin.png Protein of the Month - SGLT2 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/0b8d7732-d9c7-43bb-8b37-3b2d23ad4528/superposition.png Protein of the Month - SGLT2 in complex with the inhibitor empagliflozin https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ce2b427c-a5cb-4d7a-98d0-18a60836ea14/interactions+with+residues.png Protein of the Month - SGLT2 Image 2. Molecular interactions between hSGLT2 and empagliflozin (cartoon and lateral residues in white, ligand in blue; PDB: 7vsi). The sugar moiety of the inhibitor stacks with Tyr-290 and makes polar contacts with Asn-75 and Glu-99. The aglycone tail forms aromatic interactions with His-80 and Phe-98 and hydrophobic contacts with several residues, for instance Leu-84 and Val-95. The interactions are automatically calculated by the 3decision® software. https://3decision.discngine.com/protein-of-the-month-collection/2023/1/13/tyk2 monthly 0.5 2024-11-14 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/229cf446-d4e1-4743-bd8b-cedf51b223a3/compounds+optimization.png Protein of the Month - TYK2 compound optimization for the development of the tyk2 inhibitor by Bristol Myers Squibb https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/2a9c04d6-4438-418f-b075-607bc54fd97d/Figure+1.png Protein of the Month - TYK2 Image 1. 3D structure of compound 12 in complex with TYK2-JH2 (purple; PDB: 6NZR). Astructural water mediates the interaction with the residue Arg738. The protein hinge region is indicated for reference. Electrostatic interactions in yellow, aromatic ones in blue (interactions automatically calculated by 3decision® software). Picture produced with the 3decision® software. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/557a9215-e8a9-4fa7-860d-82397fee2aad/Figure+2.png Protein of the Month - TYK2 Image 2. Comparison of the 3D structures of TYK2-JH2 in complex with compound 12 (purple; PDB: 6NZR), compound 29 (blue; PDB: 6NZQ) and deucravacitinib (white; PDB: 6NZP). The original structural water and the optimized substituent are indicated. Picture is produced with the superposition feature and highlight mode of the 3decision® software. https://3decision.discngine.com/protein-of-the-month-collection/2022/12/1/btk monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/80455c20-b7b3-4d7e-874c-9fbb0c8e5ff9/1A.png Protein of the Month - BTK Triazolone fragment 6, a potential BTK kinaze inhibitor coming from the fragment-based drug discovery campaign https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/03f617f3-ff1e-4ea0-aae8-8123f8d3e4a8/1B.png Protein of the Month - BTK Possibility to grow the triazolone fragment 6, a BTK inhibitor hit compound coming from the fragment-based drug discovery campaign https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/5b3fdacb-2ac4-4c3e-bc3c-cce5f9e40395/2.png Protein of the Month - BTK Image 2. Overlay of the 3D structures of compounds 18 and TAK-020. Measurement of the distance between compound 18 and Cys 481 helped to select the proper chemical moiety to fill the space in the pocket (BTK complex with: 18 in white, PDB: 7N5X; TAK-020 in blue, PDB: 7N5Y). Pictures produced with 3decision® software. https://3decision.discngine.com/protein-of-the-month-collection/2022/10/28/hdac monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/a3f82219-d5c8-4c93-8419-cc339c434e0e/image+1.png Protein of the Month - HDAC Image 1: On the left: molecular structure of compound 7, and description of the different chemical moieties (the molecule was drawn in the ChemAxon sketcher in 3decision®). On the right: 3D structure of the complex of 7 with HDAC2, interacting with the zinc ion (7 in white, HDAC2 in orange, zinc in light blue; PDB: 6WBW. Picture produced with 3decision® software). https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/57e259bc-5b7f-40e4-8152-0ad49f8a2d8f/image+2v2.png Protein of the Month - HDAC Image 2. Structure-guided optimization of HDAC inhibitors: in green is shown the modification for the removal of the zinc-binding moiety; in blue, the changes in a portion of the protein-surface interacting moiety; in orange, the final modification to put a polar group in the solvent-exposed part of the inhibitor. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b0d52dbe-e38c-4ff4-9af5-014baa0b52a2/image+3.1a.png Protein of the Month - HDAC https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/cbde87c0-e229-4dde-a823-f28de8a4ac32/image+3.2.png Protein of the Month - HDAC https://3decision.discngine.com/protein-of-the-month-collection/2022/9/29/s1pr1 monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/13dddfcb-6cf5-43c9-9be7-26d03427cbd5/mesh%2Bresidues.png Protein of the Month - S1PR1 Image 1. The agonist siponimod (in yellow) bound to S1PR1 (in pink, PDB ID: 7EO4) superimposed to the same receptor in complex with an antagonist (in grey, PDB ID: 3V2Y). The differences between the two structures are highlighted using Pocket highlight mode, 3decision software. https://3decision.discngine.com/protein-of-the-month-collection/2022/8/16/atad2 monthly 0.5 2024-11-14 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/3aa7e2e0-904c-44e5-b54d-4e79dfdecf36/Image+1.png Protein of the Month - ATAD2 Image 1. Image is done with the Annotation Browser of the 3decision software. ATAD2 (PDB ID: 5LJ0) possesses an ATPase domain (red rectangle in Pfam line) and a bromodomain (blue rectangle in Pfam line). These annotations are coming from the Pfam database. The protein structure is colored corresponding to the selection. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c2486a37-d7f0-4a11-bf50-75cf2acbf41f/Image+2+-+Copy.png Protein of the Month - ATAD2 Image 2. Structure of compound 6, sketched with 3decision molecule editor (powered by ChemAxon). https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/0f534bbd-3752-4322-bce8-3e6e1d37c925/Image+3.png Protein of the Month - ATAD2 Image 3. Compound 6 bound to ATAD2 (in orange, PDB ID: 5LJ0) and to BRD4 (in blue, PDB ID: 5LJ1). The differences between the two structures are highlighted using Full Structure highlight mode, 3decision software. The binding site of BRD4 is represented by a blue mesh. The three residues constituting the WPF shelf of BRD4 BD1 are in white sticks. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/41dfab58-217e-4eee-aede-622e656e5f9b/Image+2.png Protein of the Month - ATAD2 Image 4: Structures of compound 6 and compound 26, its tropane analogue (circled in blue). Positions of C3’ and C5’ are indicated on the structures. Chemical structures were sketched with 3decision molecule editor (powered by ChemAxon). https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/39ce2ecb-5313-4efb-892f-fb132b9140d2/Image+4.png Protein of the Month - ATAD2 Image 5. Compound 6 and compound 26 bound to BRD4 (PDB ID: respectively 5JL1 in blue and 6HDQ in light grey), relocation of tryptophane W81 is highlighted. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/191f73a2-74f3-4c54-9611-c4c45f8e21f7/Image+5.png Protein of the Month - ATAD2 Image 6. Compound 6 bound to ATAD2 (orange, PDB ID: 5LJ0) and compound 26 bound to BRD4 (blue, PDB ID: 6HDQ). Location of leucine Leu94 close to C5’ position is highlighted. Val1018 is less bulky and leaves more space for ligands (see molecular surface of ATAD2 in orange). https://3decision.discngine.com/protein-of-the-month-collection/2022/7/27/malt1 monthly 0.5 2024-11-13 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/9214123f-4cd1-4ae9-a665-02badc29a225/catalytic+site+-+no+background+no+sticks.png Protein of the Month - MALT1 Image 1. Different conformations of the MALT1 catalytic site: the active conformation (structure in yellow, PDB ID: 3V4O) is disrupted both by the binding of the orthosteric ligand (structure in orange, PDB ID: 6YN8) and the distant allosteric ligand (structure in blue, PDB ID: 6YN9; ligand not shown). E500 is selected as reference residue in the three structures. The image was prepared with 3decision highlight mode: only differences among the structures are displayed. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/311f944e-4649-407c-9691-c0341259d2cd/Allosteric+pocket+V2.png Protein of the Month - MALT1 Image 2. Superposition of the allosteric pocket with ligand bounded (structure in purple, a ligand in orange, PDB ID: 6YN9) and apo inactive structure (structure in white, PDB ID: 3V55). The residue W580 in the inactive conformation is located inside the pocket. The ligand replaces this residue and stabilizes the protein in its inactive conformation. The picture is taken with 3decision - a protein structure repository and data management tool. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/a7049457-fea7-46f4-8a71-0884fcdc95fb/LeadOpt_pic1.jpg Protein of the Month - MALT1 Image 3. Lead optimization steps - from compound 2 to compound 7 https://3decision.discngine.com/protein-of-the-month-collection/2022/6/29/b-raf monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1c9c7136-5d12-49ef-8f67-d8edb6d3ca73/Picture1a.png Protein of the Month - B-RAF Image 1. Dabrafenib in complex with PXR nuclear receptor. Its tert-butyl substituent is in a hydrophobic subpocket formed by F288, W299 and Y306. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/f8dd7945-9b4d-4eb2-a827-1897a0b17a23/Picture2.png Protein of the Month - B-RAF Image 2. Superposition of B-RafV600E in complex with dabrafenib (4XV2, orange) and CQE (4CQE, blue). The cyclopropylpiperidine moiety is pointing toward the solvent. https://3decision.discngine.com/protein-of-the-month-collection/2022/5/13/glp-1r monthly 0.5 2024-11-13 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/79f4709c-f9dc-4585-b653-764bec695984/PF+water+%2B+ed+-+circle.png Protein of the Month - GLP-1R Image 1: The water-mediated polar network of Pfizer’s ligand (PF 06882961) with similar interactions with the target as its native ligand GLP-1 (PDB structure: 6X1A) https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/f0de16fa-d1b9-4aba-84d1-bec086a6b32a/CHU+%2B+ed+circle.png Protein of the Month - GLP-1R Image 2: The absence of water network in GLP-1R structure with CHU-128 compared to the one with PF 06882961 (PDB structure:6X19). The open conformation causes the increased transport of water molecules which is confirmed with the weak density on the cryoEM map. https://3decision.discngine.com/protein-of-the-month-collection/2022/5/4/tubulin monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/d222b4b2-436b-46f6-b9be-0ffdcc45a4da/image+1.2.png Protein of the Month - Tubulin Image 1: Fragment F04 co-crystallized in sID βαII binding site. The hydrophobic pocket in the αTub2 monomer with 3 structural water molecules is circled in orange. The image is prepared in the 3D Viewer of the 3decision knowledge management platform. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/29f1b018-8a04-4cb8-95f1-c998b0c0a605/image2+%281%29.png Protein of the Month - Tubulin Image 2: Superposition of subpocket fragments F04 (in red) and F36 (in blue). https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/bcbe5f5d-469e-4354-8453-f1c9edde3cc1/image3.png Protein of the Month - Tubulin Image 3: Superposition of F04 (in red) and F41 (in white). https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/9a83918c-f7f0-4c9d-8fe0-9ce5541cf5fc/image+4.png Protein of the Month - Tubulin Image 4: Todalam - a novel small molecule tubulin Inhibitor fully designed with rational structure-based approach. https://3decision.discngine.com/protein-of-the-month-collection/2022/4/14/helios monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1b24ea6d-ca84-43b2-bb6a-c6ef654fe5fb/POM_April2022+-+Copy.PNG Protein of the Month - Helios Left side: Comparison of Ikaros and Helios protein sequences, pocket view. Right side: Binding site of Cereblon/Ikaros (PDB structure 6H0F), with a highlight on Gln146 in the 3D viewer. ligand-protein interactions are shown by dashed lines. The comparison was done with 3decision - a protein structure repository that allows you to easily perform 2D and 3D pocket comparisons. https://3decision.discngine.com/protein-of-the-month-collection/2022/3/15/fgf21 monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/318f888a-dc00-4c4e-98f5-e1812b5dee56/3decision_3dviewer_image+final.png Protein of the Month - FGF21 Fibroblast growth factor 21 (FGF21) beta 2 and 3 hairpin domain https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/5b419bc6-8787-4e7e-b3cd-218afb2c124d/3decision_3dviewer_image+final2a.png Protein of the Month - FGF21 fibroblast growth factor 21 (FGF21) beta 10-11 dynamic domain https://3decision.discngine.com/protein-of-the-month-collection/2022/2/15/sars-cov-2-mpro monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/cbcddeeb-4db0-4383-b7e4-0d3ba60bebef/3decision_3dviewer_image+%2825%29.png Protein of the Month - SARS-CoV-2 Mpro Image 1: The hydrogen bond between the ligand leucin moiety (in blue) and the glutamine residue in the main protease (Q189), was lost when the Pfizer scientists designed compound 3 (in orange) with increased oral bioavailability. This image is captured in the 3decision 3D viewer. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/742713ff-8ef3-4545-b839-5dd0ad3712bd/image+2.png Protein of the Month - SARS-CoV-2 Mpro Image 2: Comparison between the indole moiety in compound 3 (in blue) with the trifluoroacetamide moiety in the final compound (in purple). The trifluoroacetamide group protrudes into the S3 pocket and restores several polar interactions with the protein. This image is captured in the 3decision 3D viewer. https://3decision.discngine.com/protein-of-the-month-collection/2022/1/21/ox2r monthly 0.5 2024-11-15 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/f40dfbac-f0d5-4c98-b964-51907ed2afd9/FINAL1.png Protein of the Month - OX2R structure of the orexin peptide in NMR https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/3f2a7f3f-732f-4241-9b5b-9000bd64d493/FINAL2.png Protein of the Month - OX2R structure of orexin B in complex with the orexin receptor type 2 https://3decision.discngine.com/protein-of-the-month-collection/2021/12/1/patched-1 monthly 0.5 2024-03-21 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/df7c1665-425c-42e2-b862-c5d50691eb8a/picture_Final.png Protein of the Month - PTCH1 Relation of the MD derived structures https://3decision.discngine.com/protein-of-the-month-collection/2021/11/plc monthly 0.5 2024-03-21 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/4d1ed423-cda0-4860-beed-0272a35fc7b9/pic.PNG Protein of the Month - PLC-gamma 3decision - Projects with human PLC gamma structures from the PDB https://3decision.discngine.com/protein-of-the-month-collection/2021/10/egfr monthly 0.5 2024-03-21 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/0b32fa17-d147-4acd-a1b8-523b91ab173e/pom+oct.PNG Protein of the Month - EGFR 3decision Advanced Search - Click to zoom in https://3decision.discngine.com/protein-of-the-month-collection/2021/09/bcl-2 monthly 0.5 2024-11-13 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/a281c039-5653-4c45-ad64-a0e9b2d4c960/pic.PNG Protein of the Month - BCL-2 3decision Get ligands that bind in the pocket feature https://3decision.discngine.com/protein-of-the-month-collection/2021/08/yes-kinase monthly 0.5 2024-03-21 https://3decision.discngine.com/protein-of-the-month-collection/2021/07/pde5 monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c2e739b9-4981-45e9-b47a-9ed39aa4da20/POM+July.PNG Protein of the Month - PDE5 Interaction based search: on the left the interactions used as query and the parameters for the search are displayed, while on the right the reference structure (PDB ID: 4h24) and one of hit structures obtained from the search are superimposed in the 3D viewer. Sildenafil (showed in violet sticks) and RBN-2397 (showed in blue sticks) form the same interaction pattern (showed as dotted lines) respectively in PDE5 and in Protein mono-ADP-ribosyl transferase PARP12. https://3decision.discngine.com/protein-of-the-month-collection/2021/06/ras-protein monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/8ed46e1e-a8b0-43fb-b9a6-94503ef10d98/pic+for+website2.PNG Protein of the Month - RAS The Ras protein. PDB ID: 6jg6 https://3decision.discngine.com/protein-of-the-month-collection/2021/05/pi3kalpha monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/f7e34b29-db25-4cf7-9fc4-d56b7f285f7c/pocket+explorer.PNG Protein of the Month - PI3K-alpha 3decision pocket explorer identifies pocket 66 as highly druggable (PDB ID: 4ovv). https://3decision.discngine.com/protein-of-the-month-collection/2021/04/brd4 monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/c6e73d97-147f-4fff-b42b-5e340b7ac3eb/POM%2BApril%2B2021.png Protein of the Month - BRD4 Collection of all 379 ligands co-crystalized in BRD4 BD1 acetyl-lysine binding site and refined set of 29 ligands that interact with selected BRD4 BD1 binding site residues (Asp144 and Ile146). https://3decision.discngine.com/protein-of-the-month-collection/2021/03/sars-cov-2-spike-protein monthly 0.5 2024-11-13 https://3decision.discngine.com/protein-of-the-month-collection/2021/02/estrogen-related-receptor-beta monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/a5c6427c-707e-49b3-b02b-b113dc47bba4/Sequence%2Bexplorer%2Band%2BHighlight%2Bmode%2Bon%2B3decision%2C%2Bestrogen%2Brelated%2Brecepter%2Bbeta.png Protein of the Month - ERR-beta 3decision Sequence Explorer allows you to combine Sequence Explorer with the 3D structural information to study ligand selectivity of ERR β LBD (PDB: 6LIT). https://3decision.discngine.com/protein-of-the-month-collection/2021/01/gaba-b-receptor monthly 0.5 2024-04-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/24190a6e-99b9-4b90-aee5-e5a7bad4d84d/pic+for+website.PNG Protein of the Month - GABA-B receptor The Annotation Browser of 3decision showing manually added sequence annotations to quickly visualize GABA-B linker region and ECL2 (PDB:7C7Q). https://3decision.discngine.com/protein-of-the-month-collection/category/Uncategorized monthly 0.5 https://3decision.discngine.com/protein-of-the-month-collection/category/POM monthly 0.5 https://3decision.discngine.com/protein-of-the-month-collection/tag/2024 monthly 0.5 https://3decision.discngine.com/protein-of-the-month-collection/tag/2023 monthly 0.5 https://3decision.discngine.com/protein-of-the-month-collection/tag/2022 monthly 0.5 https://3decision.discngine.com/protein-of-the-month-collection/tag/2021 monthly 0.5 https://3decision.discngine.com/new-events daily 0.75 2025-11-05 https://3decision.discngine.com/new-events/2025/11/9/psdi-protein-structure-determination-in-industry-meeting monthly 0.5 2025-11-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b776108b-39d4-48d4-b6a2-cfb13001165f/2502.03_hg3_psdi_banner_.jpg New Events - 33rd PSDI - “Protein Structure Determination in Industry” Conference - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/new-events/2025/3/19/discngine-labs-live-cambridge-setting-new-standards-in-sbdd monthly 0.5 2025-09-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/cf97f8cc-29cf-4eb9-ae41-1936ad4f1a15/Banner+3.png New Events - Discngine Labs Live: Setting New Standards in SBDD: Experimental and Predicted Protein Structure Synergies - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/new-events/2025/6/24/ccg-north-american-ugm-and-conference-2025 monthly 0.5 2025-09-05 https://3decision.discngine.com/new-events/2025/5/20/ccg-european-ugm-and-conference-2025 monthly 0.5 2025-09-05 https://3decision.discngine.com/new-events/2025/4/2/bio-it-world-conference-expo-2024 monthly 0.5 2025-09-05 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Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/40956ad6-01c5-4809-9c6b-384fe9214c56/Meline.png New Events - Bio-IT World Conference & Expo - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/new-events/2024/11/5/pegs-europe-protein-antibody-engineering-summit monthly 0.5 2025-09-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/9ef7631e-9ece-4d18-9794-e5034019890c/Peter.png New Events - PEGS Europe - Protein & Antibody Engineering Summit - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/new-events/2024/10/8/discngine-meetup-vol-4 monthly 0.5 2025-09-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e003a6e6-71ef-40d6-8143-ee5a427209ef/Banniere_green_FINAL.png New Events - Discngine Meetup Vol. 4 - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/new-events/2024/11/10/psdi-2024 monthly 0.5 2025-09-05 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/7c65829c-6c55-4a5d-86ec-7b06d6abc601/signature+with+date.png New Events - PSDI 2024 - 32nd Protein Structure Determination in Industry Meeting - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e3ddadfc-c105-455f-89bd-64c3b96beb01/exhibition-hall-plan-v2-only-plan.png New Events - PSDI 2024 - 32nd Protein Structure Determination in Industry Meeting - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/new-events/2023/6/20/ccg-north-american-ugm-and-conference monthly 0.5 2024-04-02 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and Conference 2023 - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/e7221406-2b2c-4c87-92a0-8a833cc8e7f9/image-asset.png New Events - CCG European UGM and Conference 2023 - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/new-events/2023/3/17/32hpwbloodclx9zit96fb9xvzvwxx0 monthly 0.5 2024-04-02 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/bd0eae7f-9e5f-4971-81a7-5a23031a70d8/BIT23-1800x940%2B%281%29.png New Events - Bio-IT World Conference & Expo 2023 - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/8734e6e8-b75a-48b9-97c1-ebee05ec62f3/Discngine%2Bfloorplan%2Bbooth%2B622+%281%29.png New Events - Bio-IT World Conference & Expo 2023 - Make 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is, the way you tell your story online can make all the difference. https://3decision.discngine.com/new-events/2022/5/18/cecam-workshop monthly 0.5 2025-07-07 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/3386de32-b30f-408d-a5b8-86546db439de/logo.png New Events - CECAM Workshop - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/new-events/2022/6/12/12th-international-conference-on-chemical-structures-iccs monthly 0.5 2024-03-14 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/340023ba-a329-4f49-a9ec-f5379e0098ea/iccs_logo.jpg New Events - 12th International Conference on Chemical Structures (ICCS) - Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/new-events/2022/5/29/chemaxon-user-meeting-europe-2022 monthly 0.5 2024-11-15 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Make it stand out Whatever it is, the way you tell your story online can make all the difference. https://3decision.discngine.com/3decision-for-molecular-modelers daily 0.75 2025-03-18 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/b45fc8ba-00ed-441f-8a88-b0cd4f7088c8/Pocket+browser.png For Modelers Explore pockets on structures | Visually explore druggable pockets on your structure https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/ba57bb61-f2d6-489a-9fa3-c48c3d123479/subpocet%2Bsearch+%281%29.png For Modelers Sub-pocket similarity search | Search for similar sub-regions of your target, create data sets and find a similar chemical matter that binds to the sub-region https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/d610e3e2-ac32-426b-bccc-f8a0cf021d8f/Interaction+search2+%281%29.png For Modelers Interaction Search | Retrieve all structures containing a specific 3D pattern of interactions to inspire your design of new compounds and flag possible off-targets. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/17eb2e90-71d3-4287-90a7-7c9737284349/annot+browser.png For Modelers Annotation Browser | Use the 3D sequence annotations to get more structural insights when visually analyzing your biomolecule. https://3decision.discngine.com/3decision-for-medicinal-chemists daily 0.75 2025-03-18 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1a2b046a-9e95-46c8-bbe4-8cc0ca255e67/search_napthalene.png For Chemists Chemistry Search | Easily sketch or import molecules to conduct chemistry-based queries against the full database. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1723829925251-TJDDQ1I2Y4MWY99GKSQM/Screenshot%2B2024-08-16%2Bat%2B09.48.51.jpg For Chemists Share Structures | Projects can be created to organize and share public or private structures with colleagues. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/2e39eff3-19b6-49fd-a130-2c3c9bafce4a/Information+Panel.png For Chemists Access knowledge | Quickly visualize and compare structures and access relevant target information. https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/15647b0f-e045-434a-9de4-5988dd40d5ab/3d_viewer_measurement.png For Chemists Measurement Options | In the 3D Viewer, quickly calculate distances, angles, and dihedrals using the measurement tools. https://3decision.discngine.com/3decision-for-structural-biologists daily 0.75 2025-03-18 https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/6c7d2557-7211-4dc6-8456-c95f68a99023/upload%2Bstructure%2BhERG+%281%29.png For Biologists Upload structure to a project | Easily deposit a new structure (Experimental or Predicted) in 3decision via the structure registration workflow in the User Interface. 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druggability and specificity https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/271272dc-7cf9-4862-98d3-000ae764c54c/DockingPose+%283%29.png 3decision® (solution) Design and dock a new ligand | Quickly dock the compound into the binding site. 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