Tak Kam Victor Wai, Goddard William A
Materials and Process Simulation Center (MC-139-74), California Institute of Technology, Pasadena, California 91125.
J Chem Theory Comput. 2008 Dec 9;4(12):2160-9. doi: 10.1021/ct800196k.
We present a new strategy for protein side-chain placement that uses flat-bottom potentials for rotamer scoring. The extent of the flat bottom depends on the coarseness of the rotamer library and is optimized for libraries ranging from diversities of 0.2 Å to 5.0 Å. The parameters reported here were optimized for forcefields using Lennard-Jones 12-6 van der Waals potential with DREIDING parameters but are expected to be similar for AMBER, CHARMM, and other forcefields. This Side-Chain Rotamer Excitation Analysis Method is implemented in the SCREAM software package. Similar scoring function strategies should be useful for ligand docking, virtual ligand screening, and protein folding applications.
我们提出了一种用于蛋白质侧链定位的新策略，该策略使用平底势来对旋转异构体进行评分。平底的范围取决于旋转异构体文库的粗糙程度，并针对多样性在0.2 Å至5.0 Å之间的文库进行了优化。这里报告的参数是针对使用带有DREIDING参数的Lennard-Jones 12-6范德华势的力场进行优化的，但预计对于AMBER、CHARMM和其他力场而言是相似的。这种侧链旋转异构体激发分析方法在SCREAM软件包中实现。类似的评分函数策略对于配体对接、虚拟配体筛选和蛋白质折叠应用应该是有用的。
