Quality Check
Scripts to analyse the quality of docking poses From Sindt and al. J. Chem. Inf. Model. 2025, 65, 11, 5553–5566
Software
LIT-AlphaFold
A new prediction pipeline called LIT-AlphaFold was developed to study the effects of template and multiple sequence alignment parameters on the results of AlphaFold and …
SpaceDock
SpaceDock is a straightforward and rapid computational approach designed to screen virtually 'ultra-large' synthetically accessible chemical libraries. It first requires docking …
ProCare
ProCare is a point cloud registration approach to align protein cavities decribed by an ensemble of 3D points. Each point is labelled with one of eight pharmacophoric features …
OCSVM-ADRB2
A new method based on the conformational dynamics of a single protein–ligand reference complex to improve the biased selection of ligands with specific pharmacological properties …
IChem
IChem is a suite of tools for detecting and comparing molecular objects (proteins, ligand-binding cavities, ligands, protein–ligand and protein–protein complexes)
SiteAlign
A method to measure distances between druggable protein cavities
Datasets
Ultra-large virtual screening hit (ULVSH) dataset
Input files (protein, active site, docking poses) of the ULVSH dataset. Two directories (raw, minimized) for raw and minimized docking poses From Sindt and al. Journal of Chemical …
PDBbind dataset 19
In-house curated input files (protein, ligand) of the PDBbind v.2019 dataset. From Volkov et al. J. Med. Chem. 2022, 65, 11, 7946–7958
LIT-PCBA
A dataset for virtual screening and machine learning. 15 target sets, 7761 actives and 382674 unique inactives selected from high-confidence PubChem Bioassay data
PPIome datasets
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
Fragdock dataset
2376 ligand/protein structures aligned describing 64 different proteins.
PDBbind datasets 14
protein-ligand complexes and Set of decoy poses from the PDBbind database. 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
Screening dataset
Virtual screening datasets: Input files for receptor and ligand database (10 actives + 990 decoys) for both the tymidine kinase and the estrogen receptor alpha from Bissantz and …