LigExtract

LigExtract processes PDB structures at large scale and identifies their associated ligands for drug discovery and biological research.

Key Features:

• End-to-end processing: Users provide a list of UniProt IDs and LigExtract returns ligand lists, individual ligand PDB files, protein chain PDB files, and log files.
• Complex ligand handling: Addresses complex ways in which ligands are stored and represented in PDB structures that other large-scale tools fail to handle.
• Decision logging: Log files record extraction decisions and flag scenarios such as covalently bound ligands for follow-up consideration.

Scientific Applications:

• Drug discovery: Enables exploration of complexed proteins and access to their associated ligands for understanding biological processes and designing new compounds of pharmaceutical interest.
• Structural biology: Supports large-scale analysis of three-dimensional macromolecular structures from the Protein Data Bank.

Methodology:

LigExtract processes PDB structures using UniProt IDs as input to identify and extract ligands, protein chains interacting with ligands, and associated metadata.