Effects of initial settings on computational protein-ligand docking accuracies for several docking programs
Effects of initial settings on computational protein-ligand docking accuracies for several docking programs
复制标题
初始设置对多个对接程序的计算蛋白质-配体对接精度的影响
DOI：
10.1080/08927022.2014.917300
复制
发表时间：
2015
影响因子：
2.1
通讯作者：
Ohgi Takahashi
中科院分区：
文献类型：
--
作者：
Akifumi Oda;Noriyuki Yamaotsu;Shuichi Hirono;Yurie Watanabe;Shuichi Fukuyoshi;Ohgi Takahashi
本研究探讨了初始设置，即初始构象、构型和对接参数对对接结果的影响。研究中使用的构象是由 CAMDAS 程序生成的。经过构象搜索计算后，根据其构象能量和相对于晶体结构的均方根偏差，从构象异构体组中选择了五个结构；例如，检索了最低能量构象异构体，以及距晶体结构最近和最远的构象异构体。使用了多个对接参数设置（默认、高速、生成 50 个姿势）。在本研究中，使用 GOLD、eHiTS、AutoDock、AutoDock vina、FRED 和 DOCK 程序进行对接计算。 GOLD、eHiTS 和 FRED 的成功率优于 AutoDock、AutoDock vina 和 DOCK。使用最远构象的对接结果比使用其他构象获得的结果差，这表明在对接计算之前应该对配体分子进行一些构象搜索。
In this study, the influences of initial settings, i.e. initial conformations, configurations and docking parameters, on docking results were investigated. The conformations used in the study were generated by the CAMDAS program. After the conformational search calculations, five structures were selected from the conformer groups according to their conformation energies and root mean square deviations against crystal structures; for example, the lowest energy conformer, as well as the closest and farthest conformers to the crystal structure, was retrieved. Several docking parameter settings were used (default, high speed, generating 50 poses). In this study, docking calculations were conducted using the GOLD, eHiTS, AutoDock, AutoDock vina, FRED and DOCK programs. The success rates of GOLD, eHiTS and FRED were better than those of AutoDock, AutoDock vina and DOCK. The docking results using the farthest conformations were worse than those obtained using other conformations, indicating that some conformation search for the ligand molecule should be performed before the docking calculations.