Deep-learning contact-map guided protein structure prediction in CASP13
Deep-learning contact-map guided protein structure prediction in CASP13
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DOI：
10.1002/prot.25792
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发表时间：
2019-08-14
影响因子：
2.9
通讯作者：
Zhang, Yang
中科院分区：
文献类型：
--
作者：
Zheng, Wei;Li, Yang;Zhang, Yang
在CASP13中，我们报告了两条全自动结构预测流水线“Zhang-Server”和“QUARK”的结果。这些管道是建立在C-I-tasser和C-Quark程序的基础上的，这两个程序又基于I-tasser和QUAK程序，但有三个新的模块：(A)新的多序列比对(MSA)生成协议，以构建用于接触预测的深层序列轮廓；(B)改进的Meta方法，NeBcon，它结合了多个接触预测器，包括ResPRE，通过耦合精度矩阵和深度剩余卷积神经网络来预测接触图；以及(C)优化的接触势，以指导结构组装模拟。对于50个缺乏同源模板的CASP13FM结构域，C-I-TASSER和C-QUARK建立的第一个模型的TM-得分分别比I-TASSER和QUARK高28%和56%。第一次，接触图预测在具有相近同源模板的TBM结构域上显示出有用的作用，其中C-I-TASSER模型的TM-分数显著高于具有P值的I-TASSER模型的TM-分数
We report the results of two fully automated structure prediction pipelines, "Zhang-Server" and "QUARK", in CASP13. The pipelines were built upon the C-I-TASSER and C-QUARK programs, which in turn are based on I-TASSER and QUARK but with three new modules: (a) a novel multiple sequence alignment (MSA) generation protocol to construct deep sequence-profiles for contact prediction; (b) an improved meta-method, NeBcon, which combines multiple contact predictors, including ResPRE that predicts contact-maps by coupling precision-matrices with deep residual convolutional neural-networks; and (c) an optimized contact potential to guide structure assembly simulations. For 50 CASP13 FM domains that lacked homologous templates, average TM-scores of the first models produced by C-I-TASSER and C-QUARK were 28% and 56% higher than those constructed by I-TASSER and QUARK, respectively. For the first time, contact-map predictions demonstrated usefulness on TBM domains with close homologous templates, where TM-scores of C-I-TASSER models were significantly higher than those of I-TASSER models with a P-value