Improving the efficiency of PSOVina for protein-ligand docking by two-stage local search

doi:10.1109/CEC.2016.7743869

Status	已發表Published
	Improving the efficiency of PSOVina for protein-ligand docking by two-stage local search
	Tai H.K.; Lin H.; Siu S.W.I.
	2016-11-14
Source Publication	2016 IEEE Congress on Evolutionary Computation, CEC 2016
Pages	770-777
Abstract	Protein-ligand docking programs are valuable tools in the modern drug discovery process for predicting the complex structure of a small molecule ligand and the target protein. Often, the configurational search algorithm in the docking tool consists of global search and local search. The former is to explore widely for promising regions in the search space and the latter is to optimize a candidate solution to a local optimum. However, accurate local search methods such as gradient-based Newton methods are very costly. In this investigation, we present a new approach to enhance the time efficiency of a docking program by introducing a two-stage local search method. Given a candidate solution, a rough local search is performed in the first stage to determine the potentiality of the solution. Only if the solution is promising, the second stage with a full local search will be performed. Our method has been realized in the PSOVina docking program and tested on two data sets. The experimental results show that two-stage local search achieves almost 2x speedup to conventional one-stage method, it also enhances the prediction performance of the docking method in terms of increased success rate and RMSD.
Keyword	BFGS Local search Optimization Protein-ligand docking PSO PSOVina
DOI	10.1109/CEC.2016.7743869
URL	View the original
Language	英語English
Fulltext Access	View Full-Text via DOI View Full-Text via Scopus
Citation statistics
Document Type	Conference paper
Collection	University of Macau
Affiliation	Universidade de Macau
First Author Affilication	University of Macau
Recommended Citation GB/T 7714	Tai H.K.,Lin H.,Siu S.W.I.. Improving the efficiency of PSOVina for protein-ligand docking by two-stage local search[C],2016:770-777.
APA	Tai H.K.,Lin H.,&Siu S.W.I..(2016).Improving the efficiency of PSOVina for protein-ligand docking by two-stage local search.2016 IEEE Congress on Evolutionary Computation, CEC 2016,770-777.

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