Kellenberger Esther, Rodrigo Jordi, Muller Pascal, Rognan Didier
Bioinformatics Group, Laboratoire de Pharmacochimie de la Communication Cellulaire, CNRS UMR7081 Illkirch, France.
Proteins. 2004 Nov 1;57(2):225-42. doi: 10.1002/prot.20149.
Eight docking programs (DOCK, FLEXX, FRED, GLIDE, GOLD, SLIDE, SURFLEX, and QXP) that can be used for either single-ligand docking or database screening have been compared for their propensity to recover the X-ray pose of 100 small-molecular-weight ligands, and for their capacity to discriminate known inhibitors of an enzyme (thymidine kinase) from randomly chosen "drug-like" molecules. Interestingly, both properties are found to be correlated, since the tools showing the best docking accuracy (GLIDE, GOLD, and SURFLEX) are also the most successful in ranking known inhibitors in a virtual screening experiment. Moreover, the current study pinpoints some physicochemical descriptors of either the ligand or its cognate protein-binding site that generally lead to docking/scoring inaccuracies.
八个可用于单配体对接或数据库筛选的对接程序（DOCK、FLEXX、FRED、GLIDE、GOLD、SLIDE、SURFLEX和QXP）已针对其恢复100个小分子量配体的X射线构象的倾向，以及区分一种酶（胸苷激酶）的已知抑制剂与随机选择的“类药物”分子的能力进行了比较。有趣的是，发现这两种特性是相关的，因为在虚拟筛选实验中显示出最佳对接准确性的工具（GLIDE、GOLD和SURFLEX）在对已知抑制剂进行排名方面也是最成功的。此外，当前研究指出了配体或其同源蛋白结合位点的一些物理化学描述符，这些描述符通常会导致对接/评分不准确。
