LigGrep

LigGrep filters docked ligand poses by user-defined receptor/ligand interaction criteria to prioritize candidate binders in structure-based virtual screening (VS).

Key Features:

• User-Specified Interaction Filters: Accepts interaction filters provided in JSON format to select poses that exhibit specified receptor/ligand interactions.
• Input Flexibility: Accepts a protein receptor file in PDB or PDBQT format and a directory of docked-compound files in PDB, PDBQT, or SDF formats.
• Pose Evaluation and Output: Evaluates each docked pose against the specified filters and outputs the names of compounds whose poses meet all criteria.

Scientific Applications:

• Virtual screening hit enrichment: Prioritizes poses that mimic key intermolecular interactions to increase the likelihood of identifying true binders in structure-based VS campaigns.
• HsPARP1 (poly(ADP-ribose) polymerase 1): Demonstrated utility by enhancing hit rates for H. sapiens poly(ADP-ribose) polymerase 1 (HsPARP1) through interaction-based pose filtering.
• HsPin1p (peptidyl-prolyl cis-trans isomerase NIMA-interacting 1): Demonstrated utility by enhancing hit rates for H. sapiens peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (HsPin1p) through interaction-based pose filtering.
• ScHxk2p (hexokinase-2): Demonstrated utility by enhancing hit rates for S. cerevisiae hexokinase-2 (ScHxk2p) through interaction-based pose filtering.

Methodology:

Evaluates docked poses against user-defined receptor/ligand interaction filters supplied in JSON and outputs compounds whose poses satisfy all specified filters.