AutoPocket2CREST: Automating Binding Pocket Extraction for the CREST Conformer Generation Pipeline

Key Points

• The aim is to develop an automated method for extracting binding pockets from protein-ligand structures to aid conformational sampling.
• Identifies ligand within protein-ligand structures
• Constructs a chemically consistent pocket around the ligand
• Applies optional backbone constraints during extraction
• Postprocesses CREST conformers to restore structural annotations
• Integrates open-source tools for reproducibility
• Enables efficient preparation of binding pockets for conformational studies
• Facilitates semiempirical conformational sampling of ligands
• Improves structural consistency in conformer generation

Abstract