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conSSert:用于准确预测有序二级结构的共识支持向量机模型。

conSSert: Consensus SVM Model for Accurate Prediction of Ordered Secondary Structure.

作者信息

Kieslich Chris A, Smadbeck James, Khoury George A, Floudas Christodoulos A

机构信息

Department of Chemical and Biological Engineering, Princeton University , Princeton, New Jersey 08544, United States.

出版信息

J Chem Inf Model. 2016 Mar 28;56(3):455-61. doi: 10.1021/acs.jcim.5b00566. Epub 2016 Mar 15.

Abstract

Accurate prediction of protein secondary structure remains a crucial step in most approaches to the protein-folding problem, yet the prediction of ordered secondary structure, specifically beta-strands, remains a challenge. We developed a consensus secondary structure prediction method, conSSert, which is based on support vector machines (SVM) and provides exceptional accuracy for the prediction of beta-strands with QE accuracy of over 0.82 and a Q2-EH of 0.86. conSSert uses as input probabilities for the three types of secondary structure (helix, strand, and coil) that are predicted by four top performing methods: PSSpred, PSIPRED, SPINE-X, and RAPTOR. conSSert was trained/tested using 4261 protein chains from PDBSelect25, and 8632 chains from PISCES. Further validation was performed using targets from CASP9, CASP10, and CASP11. Our data suggest that poor performance in strand prediction is likely a result of training bias and not solely due to the nonlocal nature of beta-sheet contacts. conSSert is freely available for noncommercial use as a webservice: http://ares.tamu.edu/conSSert/.

摘要

在大多数解决蛋白质折叠问题的方法中,准确预测蛋白质二级结构仍然是关键步骤,然而,预测有序二级结构,特别是β链,仍然是一个挑战。我们开发了一种基于支持向量机(SVM)的一致性二级结构预测方法conSSert,该方法在预测β链方面具有出色的准确性,QE准确率超过0.82,Q2-EH为0.86。conSSert使用四种表现最佳的方法(PSSpred、PSIPRED、SPINE-X和RAPTOR)预测的三种二级结构类型(螺旋、链和卷曲)的概率作为输入。conSSert使用来自PDBSelect25的4261条蛋白质链和来自PISCES的8632条链进行训练/测试。使用来自CASP9、CASP10和CASP11的目标进行了进一步验证。我们的数据表明,链预测性能不佳可能是训练偏差的结果,而不仅仅是由于β片层接触的非局部性质。conSSert作为网络服务可免费用于非商业用途:http://ares.tamu.edu/conSSert/

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