期刊
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
卷 55, 期 3, 页码 620-634出版社
WILEY
DOI: 10.1002/prot.10470
关键词
computational structure prediction; deliberately misfolded proteins; potential energy function; z scores; protein folding
资金
- NCRR NIH HHS [RR15588] Funding Source: Medline
- NIGMS NIH HHS [GM64458] Funding Source: Medline
Recent works have shown the ability of physics-based potentials (e.g., CHARMM and OPLS-AA) and energy minimization to differentiate the native protein structures from large ensemble of non-native structures. In this study, we extended previous work by other authors and developed an energy scoring function using a new set of AMBER parameters (also recently developed in our laboratory) in conjunction with molecular dynamics and the Generalized Born solvent model. We evaluated the performance of our new scoring function by examining its ability to distinguish between the native and decoy protein structures. Here we present a systematic comparison of our results with those obtained with use of other physics-based potentials by previous authors. A total of 7 decoy sets, 117 protein sequences, and more than 41,000 structures were evaluated. The results of our study showed that our new scoring function represents a significant improvement over previously published physics-based scoring functions. (C) 2004 Wiley-Liss, Inc.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据