CSAlign and CSAlign-Dock: Structure alignment of ligands considering full flexibility and application to protein–ligand docking

Autor: Sohee Kwon, Chaok Seok
Jazyk: angličtina
Rok vydání: 2023
Předmět:
Zdroj: Computational and Structural Biotechnology Journal, Vol 21, Iss , Pp 1-10 (2023)
Druh dokumentu: article
ISSN: 2001-0370
DOI: 10.1016/j.csbj.2022.11.047
Popis: Structure prediction of protein–ligand complexes, called protein–ligand docking, is a critical computational technique that can be used to understand the underlying principle behind the protein functions at the atomic level and to design new molecules regulating the functions. Protein-ligand docking methods have been employed in structure-based drug discovery for hit discovery and lead optimization. One of the important technical challenges in protein–ligand docking is to account for protein conformational changes induced by ligand binding. A small change such as a single side-chain rotation upon ligand binding can hinder accurate docking. Here we report an increase in docking performance achieved by structure alignment to known complex structures. First, a fully flexible compound-to-compound alignment method CSAlign is developed by global optimization of a shape score. Next, the alignment method is combined with a docking algorithm to dock a new ligand to a target protein when a reference protein–ligand complex structure is available. This alignment-based docking method, called CSAlign-Dock, showed superior performance to ab initio docking methods in cross-docking benchmark tests. Both CSAlign and CSAlign-Dock are freely available as a web server at https://galaxy.seoklab.org/csalign.
Databáze: Directory of Open Access Journals