Predicting protein inter-residue contacts using composite likelihood maximization and deep learning

doi:10.1186/s12859-019-3051-7

	Predicting protein inter-residue contacts using composite likelihood maximization and deep learning
	Zhang, Haicang 1,2; Zhang, Qi 1,2; Ju, Fusong 1,2; Zhu, Jianwei 1,2; Gao, Yujuan 3; Xie, Ziwei 5; Deng, Minghua 3; Sun, Shiwei 1; Zheng, Wei-Mou 4; Bu, Dongbo 1,2
	2019-10-29
发表期刊	BMC BIOINFORMATICS
ISSN	1471-2105
卷号	20 期号:1 页码:11
摘要	Background Accurate prediction of inter-residue contacts of a protein is important to calculating its tertiary structure. Analysis of co-evolutionary events among residues has been proved effective in inferring inter-residue contacts. The Markov random field (MRF) technique, although being widely used for contact prediction, suffers from the following dilemma: the actual likelihood function of MRF is accurate but time-consuming to calculate; in contrast, approximations to the actual likelihood, say pseudo-likelihood, are efficient to calculate but inaccurate. Thus, how to achieve both accuracy and efficiency simultaneously remains a challenge. Results In this study, we present such an approach (called clmDCA) for contact prediction. Unlike plmDCA using pseudo-likelihood, i.e., the product of conditional probability of individual residues, our approach uses composite-likelihood, i.e., the product of conditional probability of all residue pairs. Composite likelihood has been theoretically proved as a better approximation to the actual likelihood function than pseudo-likelihood. Meanwhile, composite likelihood is still efficient to maximize, thus ensuring the efficiency of clmDCA. We present comprehensive experiments on popular benchmark datasets, including PSICOV dataset and CASP-11 dataset, to show that: i) clmDCA alone outperforms the existing MRF-based approaches in prediction accuracy. ii) When equipped with deep learning technique for refinement, the prediction accuracy of clmDCA was further significantly improved, suggesting the suitability of clmDCA for subsequent refinement procedure. We further present a successful application of the predicted contacts to accurately build tertiary structures for proteins in the PSICOV dataset. Conclusions Composite likelihood maximization algorithm can efficiently estimate the parameters of Markov Random Fields and can improve the prediction accuracy of protein inter-residue contacts.
关键词	Residue-residue contacts prediction Deep learning Markov random fields Composite likelihood maximization
DOI	10.1186/s12859-019-3051-7
收录类别	SCI
语种	英语
资助项目	National Key Research and Development Program of China[2018YFC0910405] ; National Natural Science Foundation of China[31671369] ; National Natural Science Foundation of China[31770775] ; National Natural Science Foundation of China[31270834] ; National Natural Science Foundation of China[61272318] ; National Natural Science Foundation of China[11175224] ; National Natural Science Foundation of China[11121403] ; National Natural Science Foundation of China[3127090]
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS类目	Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
WOS记录号	WOS:000499971900001
出版者	BMC
引用统计	被引频次：10[WOS] [WOS记录] [WOS相关记录]
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/14931
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Sun, Shiwei; Zheng, Wei-Mou; Bu, Dongbo
作者单位	1.Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Informat Proc, Beijing, Peoples R China 2.Univ Chinese Acad Sci, Beijing, Peoples R China 3.Peking Univ, Sch Math Sci, Ctr Quantitat Biol, Ctr Stat Sci, Beijing, Peoples R China 4.Chinese Acad Sci, Inst Theoret Phys, Beijing, Peoples R China 5.Huazhong Univ Sci & Technol, Coll Life Sci & Technol, Wuhan, Hubei, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Haicang,Zhang, Qi,Ju, Fusong,et al. Predicting protein inter-residue contacts using composite likelihood maximization and deep learning[J]. BMC BIOINFORMATICS,2019,20(1):11.
APA	Zhang, Haicang.,Zhang, Qi.,Ju, Fusong.,Zhu, Jianwei.,Gao, Yujuan.,...&Bu, Dongbo.(2019).Predicting protein inter-residue contacts using composite likelihood maximization and deep learning.BMC BIOINFORMATICS,20(1),11.
MLA	Zhang, Haicang,et al."Predicting protein inter-residue contacts using composite likelihood maximization and deep learning".BMC BIOINFORMATICS 20.1(2019):11.