3decision’s Blog
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Stay in touch with latest news about 3decision, scientific use cases, insights from experts and more
Explore the insights from the expert panel about the current landscape, challenges, and transformative potential of AI/ML technologies in supporting antibody developability.
Can protein-protein complex models generated by AF3 effectively serve as starting points for predicting protein-protein interactions and identifying binding hotspots, thus facilitating drug design?
Using our software, 3decision®, we evaluated the accuracy of the AF3 models using Programmed cell death protein 1 (PD-1) complexes as a case study.
Gaining structural insights rapidly at the onset of a Structure-Based Drug Discovery project is key to driving the development of novel compounds. In this article, we illustrate the structure registration capabilities of 3decision® through a use case reproducing the identification of next-generation RXR targeting compounds.
Explore the insights from industry experts on how to manage vast 3D protein structures to facilitate new design ideas in SBDD
Gain valuable insights into the selectivity of CLK kinase inhibitors with 3decision®. In this use case, we will show you the data sets preparation and binding mode analysis of the CLK kinase inhibitors’ using some of the 3decision’s cool features adapted to this specific scientific use case.
Following our Discngine Labs event and discussion with scientists in early drug discovery, we have summarized insights and experiences of the community on how they use AlphaFold technology to make it more suitable for drug discovery projects.
Industry experts shared their experience with the application of the Cryo-EM structures in their drug discovery projects in our Discngine Labs event. Have a look at the key take-aways and access the recording
In this use case, we will show you the structural differences between Helios and its family members that aided the design of molecular glue. We used some of 3decision’s cool features adapted to this specific scientific use case.
Quick, Flexible and Secure are just some of the advantages of 3decision AWS Quick Start for pharma and biotech. Learn more about how you can benefit from streamlined deployment of 3decision on Amazon Web Services (AWS) cloud from our cloud expert Alexandre Gillet.
Discngine and Confo Therapeutics are starting strategic collaboration to enhance GPCR drug discovery. Companies aim to further collaborate on the future development of 3decision®.
After officially announcing the partnership, Discngine and Chemaxon organized a joint event to elaborate on technical and scientific opportunities coming from joint efforts.
Integrating several of ChemAxon’s cheminformatics and biologics software components into 3decision will expand its capabilities to work on larger biological entities, in addition to the already available features for proteins and small molecules. The registration and visualization of biological entries, like antibodies or peptides, efficient data mining, and advanced analytical capabilities will be accessible.
Get to know the latest advances of five structural biology techniques and how how they impact structure-based drug discovery
Through this usecase you will get to know how to find novel chemical entities in early drug discovery using 3decision protein-ligand interaction-based search. As an example, we performed a scaffold optimization of an active compound co-crystallized with the malaria target DHODH.
The purpose of this article is to illustrate how to apply some of 3decision’s features in scientific research. For this use case, the 3decision Subpocket Similarity Search is used to suggest modifications for the optimization of a small- molecule PROTAC. The Protein-Ligand interaction coloring by statistics is then used to evaluate docking poses of new compounds. The bromodomain-containing protein 4 – cereblon complex (BRD4-CBRN) and its degrader dBET23 are used as an example.
Discngine’s 3decision team is partnering up with Nanome to bring a new dimension to structural analysis. With 3decision in VR, users will be able to entirely exploit the structural knowledge stored in 3decision in a new and advanced way to accelerate drug-design processes.
Manuel Cases Thomas, a Medicinal chemistry consultant and director at Senechaem was looking for a solution to help him use the full potential of data at hand and generate new design ideas. In this interview, he shares how 3decision® makes a difference in his daily work: from a scientific need to the impact on design ideas and successful project outcomes.
I found my way to quickly learn new software: by validating its features. In this article, I am presenting the retrospective analysis of the detection of BCR-ABL1 allosteric binding site using the 3decision Pocket Explorer feature.
The updated 3decision® version has some important new features for cross-team collaboration and structure-based drug design project management. A lot of improvements are made on the structure visualization UI as well.
This short post shows how to quickly analyze larger collections of structures and check for common and different parts among such large sets of structures.
The continuous increase in the available 3D structural data brings along changes in the medicinal chemistry field. Dr. George Sheppard, Senior Principal Research Scientist at AbbVie, shared his thoughts on the benefits for medicinal chemists using 3D information, current challenges and limitations, and proposed potential ways for improvement, in the following interview.
The construction of accurate data sets prior to the in-silico experiments is a crucial first step in many SBDD projects. In our latest webinar, we explained how 3decision® can help ease and speed up this process. For better understanding, we presented three common use cases in SBDD using our platform.
Google-owned company DeepMind has achieved to predict 3D protein shapes with high accuracy and speed using the AI program AlphaFold. Although still in the early phase, this method can have a significant impact on drug discovery, accelerating the development of new drugs. In this article, we are discussing the importance of getting ready for the new source of structural data and how to gain the most of structural knowledge.
We sat down with Dr. Alexis Denis, Ph.D. Medicinal Chemistry Director at Galapagos to collect his thoughts on the question: Should medicinal chemists use 3D molecular modeling tools?
We were able to understand how he manages the collaboration in SBDD teams, but also to understand his vision of how these positions/roles could evolve in the future.
Recently, our collaborative platform, 3decision, just saw itself complemented with two new features (subpocket search & interaction search) and a radically different User Experience (UX). This new UX, with an updated User Interface (UI), is the result of months of collaborative work between UserStudio and the 3decision team.
In order to tell the story of this project, we gathered people from both companies to answer a few questions.
The highly requested and long-awaited interaction search is finally here! Given the great amount of structural data we have at hand, the ability to mine ligand-protein complexes based on the interactions they create was a missing piece in our analytics toolbox.
Select a couple of amino acids in the binding site of your protein and retrieve, in a matter of minutes, other structures in the database which contain a similar subpocket. Similar meaning, similar features arranged similarly in 3D space. This is what the new subpocket search feature will allow you to do in the next release of 3decision!
Last year, we set out a process to improve the user experience in 3decision. After years of gathering feedback and interviewing key users, we knew it was time to address the design and workflow flaws in the user interface. With the help of User Studio, an external UI/UX design company, we went through a deep refactoring and restyling of the front-end. The resulting work will be available in the next upcoming release of 3decision (3decision v2)!
Discngine announces that Sosei Heptares will use its 3decision® software to create an unprecedented structural GPCR chemogenomics platform. 3decision® will enable Sosei Heptares to combine public and proprietary structural data and derive unique GPCR structural insights.
How can you be more efficient in deciding what compound to make next?
Read the key takeaway messages from the BAGIM panel discussion with experts from AstraZeneca and Novartis, hosted by Gabriella Jonasson, PhD.