Evaluating protein-protein interactions in AF3 predicted complexes: a PD-1 case study
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.
Leverage Experimental and in Silico 3D Protein Structures to Accelerate SBDD Projects
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.
How to best exploit 3D protein structures for ideation in SBDD
Explore the insights from industry experts on how to manage vast 3D protein structures to facilitate new design ideas in SBDD
Understanding selectivity of CLK kinase inhibitors: structural insights with 3decision®
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.
The impact of AlphaFold in drug discovery and emerging ML-methods
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.
![The future of Cryo-EM in Pharma [event highlights]](https://images.squarespace-cdn.com/content/v1/64ef89ef638a126e29aba776/1708127142264-OPP32199H0HJACJXKCMV/Discngine+Labs+promo+-+idealogo+FINAL.png)
The future of Cryo-EM in Pharma [event highlights]
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
Starting with 3decision®: exploration of Ikaros protein family – a molecular glue use case
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.
5 fast-growing techniques in structural biology and their impact on drug discovery
Get to know the latest advances of five structural biology techniques and how how they impact structure-based drug discovery
Structure-based compound design for dihydroorotate dehydrogenase - how to leverage protein-ligand interaction patterns for scaffold hopping idea generation
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.
Structure-based lead optimization of a PROTAC small-molecule in the BRD4-CRBN complex
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.
Starting with 3decision®: Allosteric pocket detection in BCR-ABL1 kinase
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.
Spotting differences in large structure collections
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.
What are the challenges for medicinal chemists when working with 3D structures? - Interview
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.
How to speed up the preparation of data sets for Structure-Based Drug Design? – Webinar Recap
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.
Getting ready for AlphaFold with 3decision®
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.
Should medicinal chemists use 3D molecular modeling tools?
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.
Discngine & UserStudio: Uplifting User Experience in life science research applications
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.
SARS-Cov-2 - part 3 - nsp1: A hopefully more detailed analysis of the cellular saboteur
My German cartesian mind (here we go with stereotypes) asks me to start with the first protein expressed by the viral genome of SARS-Cov-2, nsp1. That is, by far, not the low hanging fruit. But it is interesting to learn more about the roles of the different constituents of the virus. Nsp1 actually has also a few very interesting roles to facilitate the viral lifecycle in its host environment.
SARS-CoV-2 - part 2 - From the viral genome to protein structures
The bread and butter of every structure based drug design or drug ID effort is the need for 3D structural information of a target of interest related to the phenotypic outcome we want to alter. In the case of SARS-Cov-2 several experimental structures are already available in the RCSB PDB. Other a large scale fragment screens from the Diamond Light Source are slowly becoming available (available in the 3decision protease project for now) on public resources likes the RCSB PDB. Popular homology modelling services also already started to provide several high quality models for some of the yet not resolved structures of the viral proteome.
But let’s first have a look what the viral genome actually contains and what are currently pursued efforts.
SARS-CoV-2 - part 1 - Thriving for a systematic target and hit ID effort
Gabriella outlined in previous posts (part I & part II) a few things about SARS-Cov-2. Back at the time the crisis was still far away from our daily lives but things have changed dramatically during the last weeks. After our initial communication to make 3decision.discngine.cloud freely available for all Covid-19 related collaboration projects we were contacted independently by several volunteers from academic and industrial groups to collaborate on a global effort. At the mean time a lot of novel initiatives have seen the day and everybody is publishing blog posts (like I am right now), linkedIn articles, chemarxiv or bioarxiv preprints etc. It’s a little bit a scientific wild-west happening right now on a global scale.