A toolkit to detect, analyze and compare protein-ligand interactions License key upon request to Dr. Didier Rognan (rognan[@]unistra.fr)

Shaper method for Shape-based alignment of pharmacophore-annotated VolSite cavities (Version 2)

Shape-based alignment of pharmacophore-annotated VolSite cavities (Version 1)

A simple and fuzzy method to align and compare druggable protein binding sites (Schalon et al., Proteins, 2008). Licence file upon request to Dr. Didier Rognan (rognan[@]unistra.fr)

A novel alignment-free high-throughput algorithm to compute pairwise similarities between protein_ligand binding sites ( Weill et al. , J Chem Info Model, 2010 )

Computes molecular interaction fingerprints (Marcou et al. J Chem Info Model, 2007 )

Interaction fingerprints viewer integrated in a pymol plugin

Empirical scoring function (Rognan et al. J Med Chem, 1999 )

In-house curated input files (protein, ligand) of the PDBbind v.2019 dataset.

LIT-PCBA: A dataset for virtual screening and machine learning. Tran-Nguyen et al. J Chem Inf Model, 60, 4263-4273, 2020

Druggable cavities/Ligands at and nearby protein-protein interfaces from the Protein Data Bank. da Silva et al. J Med Chem, 60, 4263-4273, 2019

2376 ligand/protein structures aligned describing 64 different proteins.

Input/Output files for detecting PPIs and related cavities

PDBbind Test Set: 195 protein-ligand complexes (curated mol2 files). Gabel et al. J Chem Inf Model, 54, 2807-2815, 2014

Set of decoy poses (0-5 Ang. rmsd to X-ray) for the 195 PDBbind test ligands. Gabel et al. J Chem Inf Model, 54, 2807-2815, 2014

Protein, ligand and docked poses for 10 DUD-E activity classes. Gabel et al. J Chem Inf Model, 54, 2807-2815, 2014

Docking dataset: 100 input files (protein, active site, ligand) from Kellenberger and al. Protein, 2004

Input files for receptor and ligand database (10 actives + 990 decoys) for both the tymidine kinase and the estrogen receptor alpha from Bissantz and al., J Med Chem, 2000

Recover the best or all GOLD poses according yours requirements.

Marvin edit button extension is a mediawiki extension to draw compounds in Mediawiki.