NDLI: Flexible protein-ligand docking using particle swarm optimization

Content Provider	IEEE Xplore Digital Library
Author	Bo-Fu Liu Hung-Ming Chen Hui-Ling Huang Shiow-Fen Hwang Shinn-Ying Ho
Copyright Year	2003
Description	Author affiliation: Dept. of Inf. Eng., Feng Chia Univ., Taichung (Bo-Fu Liu; Hung-Ming Chen)
Abstract	Many protein-ligand docking problems attempt to predict the bound conformations of two interacting molecules. Consequently, the docking problem requires a powerful search technique to explore the translations, orientations, and each torsion until an ideal site has been found. Therefore, protein-ligand docking can be formulated as a parameter optimization problem. However, highly flexible ligands have a lot of torsions. Therefore, the optimization problem of highly flexible docking would become more difficult due to the increment of parameter number and interactions among these parameters. We proposed a novel method SODOCK based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems. PSO has significant effect on the optimization of parameters with strong interactions. A commonly used efficient local search is incorporated into SODOCK to improve the efficiency and robustness of PSO. SODOCK is efficient for both types of ligands with small and large numbers of torsions. It is shown by computer simulation that SODOCK performs well in obtaining accurate conformations, compared with some of state-of-the-art methods. Moreover, it is also shown that SODOCK is superior to AutoDock using the same energy function in AutoDock 3.05 in terms of convergence speed, robustness, and docking energy, especially for highly flexible docking problems
Starting Page	251
Ending Page	258
File Size	1783537
Page Count	8
File Format	PDF
ISBN	0780393635
DOI	10.1109/CEC.2005.1554692
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2005-09-02
Publisher Place	UK
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Particle swarm optimization Robustness Protein engineering Optimization methods Search methods Information management Power engineering and energy Bioinformatics Computer simulation Convergence
Content Type	Text
Resource Type	Article

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1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
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