A New Approach for Flexible Molecular Docking Based on Swarm Intelligence

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...

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Bibliographic Details
Published in:Mathematical problems in engineering 2015-01, Vol.2015 (2015), p.1-10
Main Authors: Zhao, Ji, Sun, Jun, Chen, Zhiguo, Wu, Xiaojun, Fu, Yi, Xu, Wenbo
Format: Article
Language:English
Subjects:
Accuracy
Algorithms
Binding
Binding energy
CAD
Computer aided design
Docking
Energy
Engineering
Free energy
Genetic algorithms
Ligands
Mathematical models
Molecular docking
Optimization
Particle swarm optimization
Proteins
Quantum physics
Search algorithms
Search methods
Swarm intelligence
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Summary: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.
ISSN:1024-123X
1563-5147
DOI:10.1155/2015/540186