LEAP: highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains.
LEAP: highly accurate prediction of protein loop conformations by integrating coarse-grained sampling and optimized energy scores with all-atom refinement of backbone and side chains.
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LEAP：高度准确地预测了蛋白质环构象，通过将粗粒抽样和优化能量评分与主链和侧链进行全部完善。
DOI：
10.1002/jcc.23509
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发表时间：
2014-02-05
影响因子：
3
通讯作者：
Zhou, Yaoqi
中科院分区：
文献类型：
--
作者：
Liang, Shide;Zhang, Chi;Zhou, Yaoqi
关键词：
Prediction of protein loop conformations without any prior knowledge (ab initio prediction) is an unsolved problem. Its solution will significantly impact protein homology and template-based modeling as well as ab initio protein-structure prediction. Here, we developed a coarse-grained, optimized scoring function for initial sampling and ranking of loop decoys. The resulting decoys are then further optimized in backbone and side-chain conformations and ranked by all-atom energy scoring functions. The final integrated technique called LEAP (Loop prediction by Energy-Assisted Protocol) achieved a median value of 2.1Å RMSD for 325 12-residue test loops and 2.0 Å RMSD for 45 12-residue loops of CASP 10 target proteins with native core structures (backbone and side chains). If all side-chain conformations in protein cores were predicted in the absence of the target loop, loop prediction accuracy only reduces slightly (0.2Å difference in RMSD for 12-residue loops in the CASP target proteins). The accuracy obtained is about 1Å RMSD or more improvement over other methods we tested. The executable file for a Linux system is freely available for academic users at http://sparks-lab.org.
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影响因子：
--
作者：
Li Y;Rata I;Chiu SW;Jakobsson E
通讯作者：
Jakobsson E
影响因子：
5.6
作者：
CHOTHIA, C;LESK, AM
通讯作者：
LESK, AM
影响因子：
2.9
作者：
Jacobson, MP;Pincus, DL;Friesner, RA
通讯作者：
Friesner, RA
影响因子：
3
作者：
BROOKS, BR;BRUCCOLERI, RE;KARPLUS, M
通讯作者：
KARPLUS, M
影响因子：
2.9
作者：
de Bakker, PIW;DePristo, MA;Blundell, TL
通讯作者：
Blundell, TL