Random drift particle swarm optimisation algorithm for highly flexible protein-ligand docking

DOI10.1016/J.JTBI.2018.08.034MaRDI QIDQ1712669zbMATH OpenOpenAlexWikidataFDO

Authors Peng Zhang

Publication date 31 January 2019

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://doi.org/10.1016/j.jtbi.2018.08.034

zbMATH Keywords

autodock softwareevolutionary computationparticle swarm optimisationprotein-ligand docking

Mathematics Subject Classification ID

Problem solving in the context of artificial intelligence (heuristics, search strategies, etc.) (68T20) Approximation methods and heuristics in mathematical programming (90C59) Software, source code, etc. for problems pertaining to biology (92-04) Biochemistry, molecular biology (92C40)

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• scientific article; zbMATH DE number 2040776
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Cites work

• scientific article; zbMATH DE number 3497315 (Why is no real title available?)
• Minimization by Random Search Techniques
• Random drift particle swarm optimization algorithm: convergence analysis and parameter selection

Cited in

(12)

• A novel conformation optimization model and algorithm for structure-based drug design
• Insights into the molecular mechanisms of protein-ligand interactions by molecular docking and molecular dynamics simulation: a case of oligopeptide binding protein
• Extra precision docking, free energy calculation and molecular dynamics simulation studies of CDK2 inhibitors
• Performance of protein-ligand docking with CDK4/6 inhibitors: a case study
• Global optimization of protein-peptide docking by a filling function method
• A combination of numeric genetic algorithm and tabu search can be applied to molecular docking
• Evaluation of the docking algorithm based on tensor train global optimization
• Optimization applications in molecular recognition
• scientific article; zbMATH DE number 2040776 (Why is no real title available?)
• Quantified uncertainty of flexible protein-protein docking algorithms
• Hybrid-genetic algorithms for flexible ligand docking
• Augmented ant colony algorithm for virtual drug discovery

Describes a project that uses

Uses Software

• AutoDock
• DeepVS
• DockingApp
• GalaxyDock
• GalaxySite
• SODOCK
• jMetalCpp
• Python

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