| 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 |
| Externí odkaz: |
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