Algorithms for Molecular Biology | |
MoDock: A multi-objective strategy improves the accuracy for molecular docking | |
Junfeng Gu1  Xu Yang1  Ling Kang2  Jinying Wu1  Xicheng Wang1  | |
[1] State Key Laboratory of Structural Analysis for Industrial Equipment, Department of Engineering Mechanics, Dalian University of Technology, Dalian 116023, China | |
[2] Department of Computer Science and Technology, Dalian Neusoft Institute of Information, Dalian 116023, China | |
关键词: Optimization; Scoring function; Molecular docking; Multi-objective; | |
Others : 1141274 DOI : 10.1186/s13015-015-0034-8 |
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received in 2013-10-28, accepted in 2015-01-08, 发布年份 2015 | |
【 摘 要 】
Background
As a main method of structure-based virtual screening, molecular docking is the most widely used in practice. However, the non-ideal efficacy of scoring functions is thought as the biggest barrier which hinders the improvement of the molecular docking method.
Results
A new multi-objective strategy for molecular docking, named as MoDock, is presented to further improve the docking accuracy with available scoring functions. Instead of simple combination of multiple objectives with fixed weight factors, an aggregate function is adopted to approximate the real solution of the original multi-objective and multi-constraint problem, which will simultaneously smooth the energy surface of the combined scoring functions. Then, method of centers and genetic algorithm are used to find the optimal solution. Tests of MoDock against the GOLD test data set reveal the multi-objective strategy improves the docking accuracy over the individual scoring functions. Meanwhile, a 70% ratio of the good docking solutions with the RMSD value below 1.0 Å outperforms other 6 commonly used docking programs, even with a flexible receptor docking program included.
Conclusions
The results show MoDock is an effective strategy to overcome the deviations brought by single scoring function, and improves the prediction power of molecular docking.
【 授权许可】
2015 Gu et al.; licensee BioMed Central.
【 预 览 】
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Figure 1. | 76KB | Image | download |
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