PRODIGY-LIG

PRODIGY-LIG predicts binding affinities of protein–small ligand complexes using atomic-level contact analysis of protein–ligand interfaces.

Key Features:

• Predictive Methodology: Employs atomic contacts and structural properties derived from protein–ligand interfaces to estimate binding affinity.
• Performance: Demonstrated top performance in blind testing, including the D3R Grand Challenge 2 where it predicted binding affinities for 102 protein–ligand complexes.
• Residue-to-Atomic Adaptation: Adapts residue-based contact analysis from PRODIGY for protein–protein complexes to atomic-level evaluations tailored to small ligands.

Scientific Applications:

• Drug discovery: Prioritizes and ranks small-molecule candidates by predicted binding affinity to protein targets.
• Molecular interaction analysis: Characterizes interaction dynamics between proteins and small molecules using interface-derived structural metrics.
• Computational benchmarking: Serves in benchmarking and validation of affinity predictors with blind-test datasets such as D3R Grand Challenge 2.

Methodology:

Performs atomic-contact-based analysis of protein–ligand interfaces using structural properties derived from the interface.