期刊
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
卷 15, 期 9, 页码 5154-5160出版社
AMER CHEMICAL SOC
DOI: 10.1021/acs.jctc.9b00309
关键词
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资金
- National Institutes of Health [R01-GM127628, R01-GM116280]
- Welch Foundation [Q1826, Q-1512]
- Gillson-Longenbaugh Foundation
- Shanghai Municipal Science and Technology Major Project [2018SHZDZX01]
Side-chain modeling plays a critical role in protein structure prediction. However, in many current methods, balancing the speed and accuracy is still challenging. In this paper, on the basis of our previous work OPUS-Rota (Protein Sci. 2008, 17, 1576-1585), we introduce a new side-chain modeling method, OPUS-Rota2, which is tested on both a 65-protein test set (DB65) in the OPUS-Rota paper and a 379-protein test set (DB379) in the SCWRL4 paper. If the main chain is native, OPUS-Rota2 is more accurate than OPUS-Rota, SCWRL4, and OSCAR-star but slightly less accurate than OSCAR-o. Also, if the main chain is non-native, OPUS-Rota2 is more accurate 'than any other method. Moreover, OPUS-Rota2 is significantly faster than any other method, in particular, 2 orders of magnitude faster than OSCAR-o. Thus, the combination of higher accuracy and speed of OPUS-Rota2 in modeling side chains on both the native and non-native main chains makes OPUS-Rota2 a very useful tool in protein structure modeling.
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