How good is automated protein docking?
How good is automated protein docking?
复制标题
DOI：
10.1002/prot.24403
复制
发表时间：
2013-12
影响因子：
2.9
通讯作者：
Vajda, Sandor
中科院分区：
文献类型：
--
作者：
Kozakov, Dima;Beglov, Dmitri;Bohnuud, Tanggis;Mottarella, Scott E.;Xia, Bing;Hall, David R.;Vajda, Sandor
关键词：
自2004年CAPRI推出以来，蛋白质对接服务器PIPPro一直参与CAPRI。本文评估了卡普里第22-27轮中46-58目标的MSPPro 2.0性能。分析导致了一些重要的意见。首先，对于中等难度的目标，RISTOPro可靠地产生可接受或中等精度的模型，这些目标也已被其他小组成功预测，并且仅对于提交的可接受模型很少的目标失败。第二，RightPro的自动对接质量非常接近最好的人类预测组，包括我们自己的提交。这一点非常重要，因为服务器必须在48小时内提交结果，并且预测应该是可重复的，而人类预测者有几周的时间，可以使用任何类型的信息。第三，虽然我们通过运行计算成本高昂的蒙特卡罗最小化模拟来改进手动提交的RISK Pro结果，但我们观察到RISK Pro正确预测的六个复合物中只有两个的准确性有显著提高。第四，在前几轮CAPRI中没有看到的新进展是，对于所有这六个目标，由CAPRIPro提供的排名最高的模型是可接受的或质量更好的，并且排名最高的模型对于六个目标中的五个目标也是最高质量的，这证实了基于簇大小的排名模型可以可靠地识别最佳的近天然构象。
The protein docking server ClusPro has been participating in CAPRI since its introduction in 2004. This paper evaluates the performance of ClusPro 2.0 for targets 46–58 in rounds 22–27 of CAPRI. The analysis leads to a number of important observations. First, ClusPro reliably yields acceptable or medium accuracy models for targets of moderate difficulty that have also been successfully predicted by other groups, and fails only for targets that have few acceptable models submitted. Second, the quality of automated docking by ClusPro is very close to that of the best human predictor groups, including our own submissions. This is very important, because servers have to submit results within 48 hours and the predictions should be reproducible, whereas human predictors have several weeks and can use any type of information. Third, while we refined the ClusPro results for manual submission by running computationally costly Monte Carlo minimization simulations, we observed significant improvement in accuracy only for two of the six complexes correctly predicted by ClusPro. Fourth, new developments, not seen in previous rounds of CAPRI, are that the top ranked model provided by ClusPro was acceptable or better quality for all these six targets, and that the top ranked model was also the highest quality for five of the six, confirming that ranking models based on cluster size can reliably identify the best near-native conformations.
登录
查看更多内容
影响因子：
5.6
作者：
Gabb, HA;Jackson, RM;Sternberg, MJE
通讯作者：
Sternberg, MJE
影响因子：
5.8
作者：
Brenke, Ryan;Hall, David R.;Kozakov, Dima
通讯作者：
Kozakov, Dima
影响因子：
14.9
作者：
Comeau, SR;Gatchell, DW;Camacho, CJ
通讯作者：
Camacho, CJ
DOI：
10.1002/prot.10390
发表时间：
2003-07-01
期刊：
PROTEINS-STRUCTURE FUNCTION AND GENETICS
影响因子：
--
作者：
Chen, R;Mintseris, J;Weng, ZP
通讯作者：
Weng, ZP
影响因子：
3
作者：
BROOKS, BR;BRUCCOLERI, RE;KARPLUS, M
通讯作者：
KARPLUS, M