Entropy-based lamarckian quantum-behaved particle swarm optimization for flexible ligand docking.

IF 2.8 4区医学 Q3 CHEMISTRY, MEDICINAL Molecular Informatics Pub Date : 2023-03-01 DOI:10.1002/minf.202200080

Qi You, Chao Li, Jun Sun, Vasile Palade, Feng Pan

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Abstract

AutoDock is a widely used software for flexible ligand docking problems since it is open source and easy to be implemented. In this paper, a novel hybrid algorithm is proposed and applied in the docking environment of AutoDock version 4.2.6 in order to enhance the accuracy and the efficiency for dockings with flexible ligands. This search algorithm, called entropy‐based Lamarckian quantum‐behaved particle swarm optimization (ELQPSO), is a combination of the QPSO with an entropy‐based update strategy and the Solis and Wet local search (SWLS) method. By using the PDBbind core set v.2016, the ELQPSO is compared with the Lamarckian genetic algorithm (LGA), Lamarckian particle swarm optimization (LPSO) and Lamarckian QPSO (LQPSO). The experimental results reveal that the corresponding docking program of ELQPSO, named as EQDOCK in this paper, has a competitive performance in dealing with the protein‐ligand docking problems. Moreover, for the test cases with different number of torsions, the EQDOCK outperforms the other three docking programs in finding docking conformations with small root mean squared deviation (RMSD) values in most cases. In particular, it has an advantage of solving highly flexible ligand docking problems over the others.

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基于熵的柔性配体对接拉马克量子粒子群优化。

AutoDock是一个广泛使用的软件，用于解决灵活的配体对接问题，因为它是开源的，易于实现。为了提高柔性配体对接的精度和效率，本文提出了一种新的混合算法，并将其应用于AutoDock 4.2.6版本的对接环境中。这种搜索算法被称为基于熵的lamarkian量子行为粒子群优化算法(ELQPSO)，它是基于熵的量子行为粒子群优化算法与Solis和Wet局部搜索(SWLS)方法的结合。利用pdbinding核心集v.2016，将ELQPSO与lamarkian遗传算法(LGA)、lamarkian粒子群优化(LPSO)和lamarkian QPSO (LQPSO)进行比较。实验结果表明，ELQPSO相应的对接程序(本文命名为EQDOCK)在处理蛋白质-配体对接问题方面具有较好的性能。此外，对于不同扭转数的测试用例，EQDOCK在大多数情况下都能找到RMSD值较小的对接构象，优于其他三种对接程序。特别是，它具有解决高度灵活的配体对接问题的优势。

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来源期刊

Molecular Informatics CHEMISTRY, MEDICINAL-MATHEMATICAL & COMPUTATIONAL BIOLOGY

CiteScore

7.30

自引率

2.80%

发文量

审稿时长

3 months

期刊介绍： Molecular Informatics is a peer-reviewed, international forum for publication of high-quality, interdisciplinary research on all molecular aspects of bio/cheminformatics and computer-assisted molecular design. Molecular Informatics succeeded QSAR & Combinatorial Science in 2010. Molecular Informatics presents methodological innovations that will lead to a deeper understanding of ligand-receptor interactions, macromolecular complexes, molecular networks, design concepts and processes that demonstrate how ideas and design concepts lead to molecules with a desired structure or function, preferably including experimental validation. The journal''s scope includes but is not limited to the fields of drug discovery and chemical biology, protein and nucleic acid engineering and design, the design of nanomolecular structures, strategies for modeling of macromolecular assemblies, molecular networks and systems, pharmaco- and chemogenomics, computer-assisted screening strategies, as well as novel technologies for the de novo design of biologically active molecules. As a unique feature Molecular Informatics publishes so-called "Methods Corner" review-type articles which feature important technological concepts and advances within the scope of the journal.