Efficient docking of peptides to proteins without prior knowledge of the binding site
Efficient docking of peptides to proteins without prior knowledge of the binding site
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DOI：
10.1110/ps.0202302
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发表时间：
2002-07-01
期刊：
影响因子：
8
通讯作者：
van der Spoel, D
中科院分区：
文献类型：
--
作者：
Hetényi, C;van der Spoel, D
配体分子与蛋白质或其他靶标对接的可靠性是分子建模的重要挑战。对接技术的应用不仅包括预测新药的结合模式，还包括蛋白质相互作用的研究等。在这里，我们提出了一个流行的AutoDock程序所获得的结果的可靠性的研究。我们已经进行了系统研究，以测试AutoDock重现8种不同蛋白质/配体复合物的能力，这些蛋白质/配体复合物的结构已知，而无需事先了解结合位点。更具体地说，我们看看影响最终结构的准确性的因素，如配体中的扭转自由度的数量。我们得出结论，Autodock程序包能够根据能量选择正确的复合物，而无需事先了解结合位点。我们将这种应用命名为盲对接，因为对接算法不能“看到”结合位点，但仍然可以找到它。盲对接的成功代表了结构基因组学时代的重要发现。
Reliability in docking of ligand molecules to proteins or other targets is an important challenge for molecular modeling. Applications of the docking technique include not only prediction of the binding mode of novel drugs, but also other problems like the study of protein-protein interactions. Here we present a study on the reliability of the results obtained with the popular AutoDock program. We have performed systematical studies to test the ability of AutoDock to reproduce eight different protein/ligand complexes for which the structure was known, without prior knowledge of the binding site. More specifically, we look at factors influencing the accuracy of the final structure, such as the number of torsional degrees of freedom in the ligand. We conclude that the Autodock program package is able to select the correct complexes based on the energy without prior knowledge of the binding site. We named this application blind docking, as the docking algorithm is not able to "see" the binding site but can still find it. The success of blind docking represents an important finding in the era of structural genomics.