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Mathematical Problems in Engineering
Volume 2015 (2015), Article ID 540186, 10 pages
Research Article

A New Approach for Flexible Molecular Docking Based on Swarm Intelligence

1Department of Electronic and Information Engineering, Wuxi City College of Vocational Technology, Wuxi, Jiangsu 214153, China
2School of Internet of Things Engineering, Jiangnan University, Wuxi, Jiangsu 214122, China

Received 29 September 2014; Accepted 23 November 2014

Academic Editor: Ezzat G. Bakhoum

Copyright © 2015 Yi Fu et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Molecular docking methods play an important role in the field of computer-aided drug design. In the work, on the basis of the molecular docking program AutoDock, we present QLDock as a tool for flexible molecular docking. For the energy evaluation, the algorithm uses the binding free energy function that is provided by the AutoDock 4.2 tool. The new search algorithm combines the features of a quantum-behaved particle swarm optimization (QPSO) algorithm and local search method of Solis and Wets for solving the highly flexible protein-ligand docking problem. We compute the interaction of 23 protein-ligand complexes and compare the results with those of the QDock and AutoDock programs. The experimental results show that our approach leads to substantially lower docking energy and higher docking precision in comparison to Lamarckian genetic algorithm and QPSO algorithm alone. QPSO-ls algorithm was able to identify the correct binding mode of 74% of the complexes. In comparison, the accuracy of QPSO and LGA is 52% and 61%, respectively. This difference in performance rises with increasing complexity of the ligand. Thus, the novel algorithm QPSO-ls may be used to dock ligand with many rotatable bonds with high accuracy.