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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, based on our previous work OPUS-Rota (Prot. Sci. (2008) 17, 1576-1585), we introduce a new side-chain modeling method, OPUS-Rota2, which is tested on both 65-protein test set (DB65) in OPUS-Rota paper and 379-protein test set (DB379) in 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. And 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 two 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.
This article was published in the following journal.
Name: Journal of chemical theory and computation
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