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Progress in super long loop prediction | |
2011 | |
发表期刊 | PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS |
ISSN | 0887-3585 |
卷号 | 79期号:10页码:2920-2935 |
发表状态 | 已发表 |
DOI | 10.1002/prot.23129 |
摘要 | Sampling errors are very common in super long loop (referring here to loops that have more than thirteen residues) prediction, simply because the sampling space is vast. We have developed a dipeptide segment sampling algorithm to solve this problem. As a first step in evaluating the performance of this algorithm, it was applied to the problem of reconstructing loops in native protein structures. With a newly constructed test set of 89 loops ranging from 14 to 17 residues, this method obtains average/median global backbone root-mean-square deviations (RMSDs) to the native structure (superimposing the body of the protein, not the loop itself) of 1.46/0.68 angstrom. Specifically, results for loops of various lengths are 1.19/0.67 angstrom for 36 fourteen-residue loops, 1.55/0.75 angstrom for 30 fifteen-residue loops, 1.43/0.80 angstrom for 14 sixteen-residue loops, and 2.30/1.92 angstrom for nine seventeen-residue loops. In the vast majority of cases, the method locates energy minima that are lower than or equal to that of the minimized native loop, thus indicating that the new sampling method is successful and rarely limits prediction accuracy. Median RMSDs are substantially lower than the averages because of a small number of outliers. The causes of these failures are examined in some detail, and some can be attributed to flaws in the energy function, such as pi-pi interactions are not accurately accounted for by the OPLS-AA force field we employed in this study. By introducing a new energy model which has a superior description of pi-pi interactions, significantly better results were achieved for quite a few former outliers. Crystal packing is explicitly included in order to provide a fair comparison with crystal structures. |
关键词 | long loop build conformational sampling computational cost |
URL | 查看原文 |
收录类别 | SCI |
语种 | 英语 |
WOS研究方向 | Biochemistry & Molecular Biology ; Biophysics |
WOS类目 | Biochemistry & Molecular Biology ; Biophysics |
WOS记录号 | WOS:000295428900011 |
WOS关键词 | SIDE-CHAIN CONFORMATIONS ; LOCAL OPTIMIZATION PROGRAM ; AB-INITIO CONSTRUCTION ; FORCE-FIELD ; POLYPEPTIDE FRAGMENTS ; MODEL ; PROTEINS ; ALGORITHM ; ACCURACY ; ENERGY |
原始文献类型 | Article |
引用统计 | |
文献类型 | 期刊论文 |
条目标识符 | https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/120121 |
专题 | 个人在本单位外知识产出 |
通讯作者 | Friesner, Richard A. |
作者单位 | 1.Columbia Univ, Dept Chem, New York, NY 10027 USA 2.Schrodinger Inc, New York, NY USA |
推荐引用方式 GB/T 7714 | Zhao, Suwen,Zhu, Kai,Li, Jianing,et al. Progress in super long loop prediction[J]. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,2011,79(10):2920-2935. |
APA | Zhao, Suwen,Zhu, Kai,Li, Jianing,&Friesner, Richard A..(2011).Progress in super long loop prediction.PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS,79(10),2920-2935. |
MLA | Zhao, Suwen,et al."Progress in super long loop prediction".PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 79.10(2011):2920-2935. |
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