Article: CSAlign and CSAlign-Dock: Structure alignment of ligands considering full flexibility and application to protein-ligand docking.
Computational and structural biotechnology journal
2022 Volume 21, Page(s) 1–10
Abstract: 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 ... ...
| Abstract | 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 |
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| Language | English |
| Publishing date | 2022-11-26 |
| Publishing country | Netherlands |
| Document type | Journal Article |
| ZDB-ID | 2694435-2 |
| ISSN | 2001-0370 |
| ISSN | 2001-0370 |
| DOI | 10.1016/j.csbj.2022.11.047 |
| Database | MEDical Literature Analysis and Retrieval System OnLINE |
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