LigTBM

LigTBM performs template-based docking of small molecules to proteins to generate structural models of protein–ligand complexes for use in drug discovery and protein–small molecule interaction prediction.

Key Features:

• Template-Based Docking Approach: Identifies known protein–ligand complexes with ligands that partially cover the target ligand to provide structural templates.
• Conformational Sampling and Template-Guided Energy Refinement: Performs extensive conformational sampling of ligand poses followed by template-guided energy refinement.
• Scoring System: Scores refined poses to rank and select top candidate binding modes.
• Integration with ClusPro Suite: Integrates with the ClusPro docking server suite for combined docking workflows.

Scientific Applications:

• Benchmarking and Validation: Evaluated on the Astex Diverse benchmark and targets from the D3R (Drug Design Data Resource) Grand Challenge.
• Drug Discovery and Interaction Prediction: Supports prediction of small-molecule binding poses for drug discovery and molecular biology research.

Methodology:

Template identification of known complexes with partial ligand overlap, extensive conformational sampling of poses, template-guided energy refinement, and scoring of refined poses; approaches adapted from CAPRI methodologies.