CAS in Crystallography and Biophysics, University of Madras, Chennai-600025, India.
J Chem Inf Model. 2009 Dec;49(12):2687-94. doi: 10.1021/ci900332a.
The theoretical prediction of the association of a flexible ligand with a protein receptor requires efficient sampling of the conformational space of the ligand. Several docking methodologies are currently available. We have proposed a docking technique that performs well at low computational cost. The method uses mutually orthogonal Latin squares to efficiently sample the docking space. A variant of the mean field technique is used to analyze this sample to arrive at the optimum. The method has been previously applied to search through both the conformational space of a peptide as well its docking space. Here we extend this method to simultaneously identify both the low energy conformation as well as a high scoring docking mode for the small organic ligand molecules. Application of the method to 45 protein-ligand complexes, in which the number of rotatable torsions varies from 2 to 19, and comparisons with AutoDock 4.0, showed that the method works well.
理论上预测柔性配体与蛋白质受体的结合需要有效地对配体的构象空间进行采样。目前有几种对接方法可用。我们提出了一种在低计算成本下表现良好的对接技术。该方法使用相互正交的拉丁方来有效地对对接空间进行采样。使用平均场技术的变体来分析此样本，以获得最佳结果。该方法以前已用于搜索肽的构象空间及其对接空间。在这里，我们将此方法扩展到同时识别小分子有机配体的低能量构象和高得分对接模式。该方法应用于 45 个蛋白质-配体复合物，其中可旋转的扭转数从 2 到 19 不等，与 AutoDock 4.0 的比较表明该方法效果良好。
