Chung Jae Yoon, Hah Jung-Mi, Cho Art E
Department of Bioinformatics and Biotechnology, Korea University, Jochiwon, Chungnam, Korea.
J Chem Inf Model. 2009 Oct;49(10):2382-7. doi: 10.1021/ci900231p.
Use of SiteMap for binding site classification and its connection to QM/MM (quantum mechanics/ molecular mechanics) docking performance were investigated. Using the hydrophilic/hydrophobic character values along with balance between them which SiteMap calculates, we sorted 455 cocrystal complexes available from protein data bank into three groups and tested how Glide, a conventional docking program, and QPLD, a QM/MM docking program, perform on them. QPLD showed improvements on all three groups over Glide but with varying degrees. Analysis of the results was carried out, and establishment of correlations between the classification of binding sites and QM/MM docking performance was attempted. It was found that QM/MM docking delivers the most improvements for primarily hydrophobic binding sites with substantial hydrophilic interactions. Based on our findings, we make suggestions for use of QM/MM docking and directions for further developments.
研究了使用SiteMap进行结合位点分类及其与量子力学/分子力学（QM/MM）对接性能的关联。利用SiteMap计算出的亲水性/疏水性特征值及其之间的平衡，我们将从蛋白质数据库中获取的455个共晶复合物分为三组，并测试了传统对接程序Glide和QM/MM对接程序QPLD在这些复合物上的表现。QPLD在所有三组上相对于Glide都有改进，但程度不同。对结果进行了分析，并尝试建立结合位点分类与QM/MM对接性能之间的相关性。发现QM/MM对接对于主要为疏水性且具有大量亲水性相互作用的结合位点改进最大。基于我们的发现，我们对QM/MM对接的使用提出建议以及进一步发展的方向。
