Computational Chemistry/Biochemistry/Biophysics list of tools
https://admet.if-pan.krakow.pl/ - "ADMET analysis"
https://github.com/NiBoyang/AutoDock-SS - "AutoDock-SS is a novel algorithm designed for ligand-based virtual screening. It leverages advanced computational techniques to efficiently screen large compound libraries against a reference ligand, facilitating the discovery of potential drug candidates"
https://github.com/xichengeva/DeepGlycanSite - "Highly accurate carbohydrate-binding site prediction with DeepGlycanSite" Nature Comm
https://www.biorxiv.org/content/10.1101/2024.06.03.597105v1 - "Protein Design with StructureGPT: a Deep Learning Model for Protein Structure-to-Sequence Translation"
https://fraggrow.xundrug.cn/ - "FragGrow: A Web Server for Structure-Based Drug Design by Fragment Growing within Constraints"
https://chemrxiv.org/engage/chemrxiv/article-details/661fec7f418a5379b00ae036 - "MolPipeline : A python package for processing molecules with RDKit in scikit-learn"
https://github.com/porekhov/CG_probeMD - "Colabind: A Cloud-Based Approach for Prediction of Binding Sites Using Coarse-Grained Simulations with Molecular Probes"
https://github.com/GHeinzelmann/BAT.py - "BAT2: An open-source tool for flexible, automated and low cost absolute binding free energy calculations"
https://github.com/azamanos/HydraProt - "HydraProt: A New Deep Learning Tool for Fast and Accurate Prediction of Explicit Water Positions for Protein Structures"
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-023-00703-1 - "VSFlow: an open-source ligand-based virtual screening tool"
https://jcheminf.biomedcentral.com/articles/10.1186/s13321-019-0358-3 - "Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening"
https://github.com/LBLQMM/MACAW - "MACAW, cheminformatic tool for Python that embeds molecules in a low-dimensional, continuous numerical space. It also enables the generation of new molecules on specification."
https://github.com/mqcomplab/MDANCE - "Molecular Dynamics Analysis with N-ary Clustering Ensembles (MDANCE)"
https://github.com/IFMlab/ChemFlow - ChemFlow is a series of drug discovery workflows