FitDock: protein–ligand docking by template fitting

Abstract Protein–ligand docking is an essential method in computer-aided drug design and structural bioinformatics. It can be used to identify active compounds and reveal molecular mechanisms of biological processes. A successful docking usually requires thorough conformation sampling and scoring, w...

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Vydané v:Briefings in bioinformatics Ročník 23; číslo 3
Hlavní autori: Yang, Xiaocong, Liu, Yang, Gan, Jianhong, Xiao, Zhi-Xiong, Cao, Yang
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: England Oxford University Press 13.05.2022
Oxford Publishing Limited (England)
Predmet:
Bioinformatics
Biological activity
CAD
Computer aided design
Crystal structure
Docking
Drug development
Ligands
Molecular modelling
Proteins
protein–ligand docking
molecular alignment
structure prediction
ISSN:1467-5463, 1477-4054, 1477-4054
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Shrnutí:Abstract Protein–ligand docking is an essential method in computer-aided drug design and structural bioinformatics. It can be used to identify active compounds and reveal molecular mechanisms of biological processes. A successful docking usually requires thorough conformation sampling and scoring, which are computationally expensive and difficult. Recent studies demonstrated that it can be beneficial to docking with the guidance of existing similar co-crystal structures. In this work, we developed a protein–ligand docking method, named FitDock, which fits initial conformation to the given template using a hierarchical multi-feature alignment approach, subsequently explores the possible conformations and finally outputs refined docking poses. In our comprehensive benchmark tests, FitDock showed 40%–60% improvement in terms of docking success rate and an order of magnitude faster over popular docking methods, if template structures exist (> 0.5 ligand similarity). FitDock has been implemented in a user-friendly program, which could serve as a convenient tool for drug design and molecular mechanism exploration. It is now freely available for academic users at http://cao.labshare.cn/fitdock/.
Bibliografia:ObjectType-Article-1
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ISSN:1467-5463
1477-4054
1477-4054
DOI:10.1093/bib/bbac087