Public
This directory contains 9 workflows.
4D-QSAR ML Both Binding and 2D Features
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4D-QSAR ML Only Binding Features
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Assessment of Vina for SARS-CoV-2 Main Protease
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Binding site shape clustering
Analyze a set of PDB structures (or a molecular dynamics trajectory) with SiteMap to characterize frames for possible binding sites. Performed volume […]
Database preparation 1-3
Label compounds from a single vendor. Prepare and filter compounds by various criteria. Based on: Clark, D.E.; Higgs, C.; Wren, S.P.; Dyke, H.J.; Wong, M.; […]
MMP FEP input preparation
This workflow takes as inputs: a list of PDB structure IDs, corresponding cocrystallized ligand and Matched Molecular Pair smiles. It downloads the […]
Reaction-based enumeration
Enumerate structures by substitution of R groups in the reactants and products of a single- or multi-step reaction. It is also use for Core hopping.
Sitemap and docking
Prepare a set of PDB structures and identify possible binding sites with Sitemap. Generate receptor grids with Glide for each site and used to dock […]