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Molecules 2017, 22(12), 2233; doi:10.3390/molecules22122233

HIGA: A Running History Information Guided Genetic Algorithm for Protein–Ligand Docking

Key Laboratory of Medical Image Computing of Northeastern University, Ministry of Education, and School of Computer Science and Engineering, Northeastern University, Shenyang 110819, China
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Received: 8 November 2017 / Revised: 3 December 2017 / Accepted: 12 December 2017 / Published: 15 December 2017
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Abstract

Protein-ligand docking is an essential part of computer-aided drug design, and it identifies the binding patterns of proteins and ligands by computer simulation. Though Lamarckian genetic algorithm (LGA) has demonstrated excellent performance in terms of protein-ligand docking problems, it can not memorize the history information that it has accessed, rendering it effort-consuming to discover some promising solutions. This article illustrates a novel optimization algorithm (HIGA), which is based on LGA for solving the protein-ligand docking problems with an aim to overcome the drawback mentioned above. A running history information guided model, which includes CE crossover, ED mutation, and BSP tree, is applied in the method. The novel algorithm is more efficient to find the lowest energy of protein-ligand docking. We evaluate the performance of HIGA in comparison with GA, LGA, EDGA, CEPGA, SODOCK, and ABC, the results of which indicate that HIGA outperforms other search algorithms. View Full-Text
Keywords: running history information; drug design; genetic algorithm; protein-ligand docking running history information; drug design; genetic algorithm; protein-ligand docking
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Guan, B.; Zhang, C.; Zhao, Y. HIGA: A Running History Information Guided Genetic Algorithm for Protein–Ligand Docking. Molecules 2017, 22, 2233.

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