A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking.
A force field with discrete displaceable waters and desolvation entropy for hydrated ligand docking.
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DOI：
10.1021/jm2005145
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发表时间：
2012-01-26
影响因子：
7.3
通讯作者：
Olson, Arthur J.
中科院分区：
文献类型：
--
作者：
Forli, Stefano;Olson, Arthur J.
In modeling ligand-protein interactions, the representation and role of water is of great importance. We introduce a forcefield and hydration docking method that enables the automated prediction of waters mediating the binding of ligands with target proteins. The method presumes no prior knowledge of the apo or holo protein hydration state, and is potentially useful in the process of structure-based drug discovery. The hydration forcefield accounts for the entropic and enthalpic contributions of discrete waters to ligand binding, improving energy estimation accuracy and docking performance. The forcefield has been calibrated and validated on a total of 417 complexes (197 training set; 220 test set), then tested in cross-docking experiments, for a total of 1649 ligand-protein complexes evaluated. The method is computationally efficient and was used to model up to 35 waters during docking. The method was implemented and tested using unaltered AutoDock4 with new forcefield tables.
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