FIPSDock: A new molecular docking technique driven by fully informed swarm optimization algorithm

Yu Liu, Lei Zhao, Wentao Li, Dongyu Zhao, Miao Song, Yongliang Yang

Research output: Journal article publicationJournal articleAcademic researchpeer-review

43 Citations (Scopus)

Abstract

The accurate prediction of protein-ligand binding is of great importance for rational drug design. We present herein a novel docking algorithm called as FIPSDock, which implements a variant of the Fully Informed Particle Swarm (FIPS) optimization method and adopts the newly developed energy function of AutoDock 4.20 suite for solving flexible protein-ligand docking problems. The search ability and docking accuracy of FIPSDock were first evaluated by multiple cognate docking experiments. In a benchmarking test for 77 protein/ligand complex structures derived from GOLD benchmark set, FIPSDock has obtained a successful predicting rate of 93.5% and outperformed a few docking programs including particle swarm optimization (PSO)@AutoDock, SODOCK, AutoDock, DOCK, Glide, GOLD, FlexX, Surflex, and MolDock. More importantly, FIPSDock was evaluated against PSO@AutoDock, SODOCK, and AutoDock 4.20 suite by cross-docking experiments of 74 protein-ligand complexes among eight protein targets (CDK2, ESR1, F2, MAPK14, MMP8, MMP13, PDE4B, and PDE5A) derived from Sutherland-crossdock-set. Remarkably, FIPSDock is superior to PSO@AutoDock, SODOCK, and AutoDock in seven out of eight cross-docking experiments. The results reveal that FIPS algorithm might be more suitable than the conventional genetic algorithm-based algorithms in dealing with highly flexible docking problems.
Original languageEnglish
Pages (from-to)67-75
Number of pages9
JournalJournal of Computational Chemistry
Volume34
Issue number1
DOIs
Publication statusPublished - 5 Jan 2013
Externally publishedYes

Keywords

  • conformational sampling
  • cross-docking
  • docking accuracy
  • flexible docking
  • protein-ligand binding

ASJC Scopus subject areas

  • Chemistry(all)
  • Computational Mathematics

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