Automated docking to multiple target structures:: Incorporation of protein mobility and structural water heterogeneity in AutoDock
Automated docking to multiple target structures:: Incorporation of protein mobility and structural water heterogeneity in AutoDock
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DOI：
10.1002/prot.10028
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发表时间：
2002-01-01
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影响因子：
--
通讯作者：
Goodsell, DS
中科院分区：
文献类型：
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作者：
Österberg, F;Morris, GM;Goodsell, DS
使用蛋白质结构合奏，在配体船上模拟中近似结构水的蛋白质运动和异质性。测试了将多个目标结构组合在单个基于网格的相互作用能量表中的四种方法。使用21种肽型抑制剂具有人类免疫缺陷病毒1型（HIV-1）蛋白酶的复合物评估该方法。这些结构中有几种显示了精氨酸残基的运动，这对于大抑制剂的结合至关重要。在20个结构中也存在结构性水，但其余的水必须不存在以进行适当的结合。均值和最小方法的性能较差，但是两种加权平均方法允许使用目标蛋白结构的单个网格表示，可以保持一致，准确的配体对接。蛋白质2002; 46：34-40。 （c）2001 Wiley-Liss，Inc。
Protein motion and heterogeneity of structural waters are approximated in ligand-docking simulations, using an ensemble of protein structures. Four methods of combining multiple target structures within a single grid-based lookup table of interaction energies are tested. The method is evaluated using complexes of 21 peptidomimetic inhibitors with human immunodeficiency virus type 1 (HIV-1) protease. Several of these structures show motion of an arginine residue, which is essential for binding of large inhibitors. A structural water is also present in 20 of the structures, but it must be absent in the remaining one for proper binding. Mean and minimum methods perform poorly, but two weighted average methods permit consistent and accurate ligand docking, using a single grid representation of the target protein structures. Proteins 2002;46:34-40. (C) 2001 Wiley-Liss, Inc.