Interested in the new developments of deep learning in virtual screening ? Check out our review Kimber, 2021. We discuss ligand, protein and complex encodings, deep learning models, data sets, and recent studies. If you want to generate different encodings for your figures, have a look at the GitHub repository!
The new edition of the “Structural Alignment and Superposition” internship is now open for registration! In this internship, an open-source structural alignment Python package for biopolymers, i.e. proteins and ligands, that we started implementing in 2020 will be further developed and released. While diverse structural alignment implementations can be found in visualization software such as PyMol, VMD or UCSF Chimera, a standalone package is currently missing in the Python ecosystem. We have started filling that gap with a modern Python package designed under the current best practices for development, testing and deployment.
Our KinFragLib project is now published in the Journal of Chemical Modeling and Information: “KinFragLib: Exploring the Kinase Inhibitor Space Using Subpocket-Focused Fragmentation and Recombination” (DOI: 10.1021/acs.jcim.0c00839). Kinases are one of the most studied drug targets, resulting in an amount of available data too large to be analyzed manually. In the KinFragLib project, a precise cartography of the ATP-binding site guides the fragmentation of cocrystallized kinase ligands by subpockets. The resulting kinase-focused fragment library allows the analysis of the chemical space by subpocket and is a rich source of inspiration for building novel kinase inhibitors.
We are happy to present the results of our KinFragLib project. Aiming to explore and extend the chemical space of kinase inhibitors, we propose a novel subpocket-guided fragmentation and recombination strategy. Take a look at our preprint on ChemRxiv to find our more: “KinFragLib: Exploring the kinase inhibitor space using subpocket-focused fragmentation and recombination”. You can find the reported fragment and combinatorial libraries including all analyses notebooks on our GitHub repository.
For obvious reasons, this edition will be online. It will take place on 2020.07.23. Check the struc2drug section for more details!
We have been working on our new website for a few months and we can finally say that we are happy to announce we are going live! Special thanks to Jaime Rodríguez-Guerra for putting this together!
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