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GM-DockZn: a geometry matching-based docking algorithm for zinc proteins.
Bioinformatics ( IF 5.8 ) Pub Date : 2020-05-05 , DOI: 10.1093/bioinformatics/btaa292
Kai Wang 1, 2 , Nan Lyu 1 , Hongjuan Diao 1 , Shujuan Jin 3, 4 , Tao Zeng 1 , Yaoqi Zhou 3, 4, 5 , Ruibo Wu 1, 5
Affiliation  

Molecular docking is a widely used technique for large-scale virtual screening of the interactions between small-molecule ligands and their target proteins. However, docking methods often perform poorly for metalloproteins due to additional complexity from the three-way interactions among amino-acid residues, metal ions and ligands. This is a significant problem because zinc proteins alone comprise about 10% of all available protein structures in the protein databank. Here, we developed GM-DockZn that is dedicated for ligand docking to zinc proteins. Unlike the existing docking methods developed specifically for zinc proteins, GM-DockZn samples ligand conformations directly using a geometric grid around the ideal zinc-coordination positions of seven discovered coordination motifs, which were found from the survey of known zinc proteins complexed with a single ligand.

中文翻译:

GM-DockZn:基于几何匹配的锌蛋白对接算法。

分子对接是一种广泛使用的技术,用于大规模虚拟筛选小分子配体与其靶蛋白之间的相互作用。但是,由于氨基酸残基,金属离子和配体之间的三向相互作用增加了额外的复杂性,对接方法对于金属蛋白的性能通常较差。这是一个重大问题,因为仅锌蛋白就构成了蛋白质数据库中所有可用蛋白质结构的约10%。在这里,我们开发了专用于配体对接锌蛋白的GM-Dock Zn。与现有专门为锌蛋白开发的现有对接方法不同,GM-Dock Zn 直接在7个发现的配位基序的理想锌配位位置周围使用几何网格对配体构象进行采样,这是从已知与单个配体复合的锌蛋白的调查中发现的。
更新日期:2020-07-03
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