ITP OpenIR  > 2017年知识产出
Improving prediction of burial state of residues by exploiting correlation among residues
Gong, HE; Zhang, HC; Zhu, JW; Wang, C; Sun, SW; Zheng, WM; Bu, DB; Bu, DB (reprint author), Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Proc, Beijing 100190, Peoples R China.; Zheng, WM (reprint author), Chinese Acad Sci, Inst Theoret Phys, Beijing 100190, Peoples R China.
2017
发表期刊BMC BIOINFORMATICS
卷号18页码:70
文章类型Article
摘要Background: Residues in a protein might be buried inside or exposed to the solvent surrounding the protein. The buried residues usually form hydrophobic cores to maintain the structural integrity of proteins while the exposed residues are tightly related to protein functions. Thus, the accurate prediction of solvent accessibility of residues will greatly facilitate our understanding of both structure and functionalities of proteins. Most of the state-of-the-art prediction approaches consider the burial state of each residue independently, thus neglecting the correlations among residues. Results: In this study, we present a high-order conditional random field model that considers burial states of all residues in a protein simultaneously. Our approach exploits not only the correlation among adjacent residues but also the correlation among long-range residues. Experimental results showed that by exploiting the correlation among residues, our approach outperformed the state-of-the-art approaches in prediction accuracy. In-depth case studies also showed that by using the high-order statistical model, the errors committed by the bidirectional recurrent neural network and chain conditional random field models were successfully corrected. Conclusions: Our methods enable the accurate prediction of residue burial states, which should greatly facilitate protein structure prediction and evaluation.
关键词Protein Structure Burial States Of Residue Conditional Random Field Residue Correlation
学科领域Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
资助者National Basic Research Program of China [2012CB316502] ; National Basic Research Program of China [2012CB316502] ; National Natural Science Foundation of China [11175224, 11121403, 31270834, 61272318, 31671369] ; National Natural Science Foundation of China [11175224, 11121403, 31270834, 61272318, 31671369] ; National Basic Research Program of China [2012CB316502] ; National Basic Research Program of China [2012CB316502] ; National Natural Science Foundation of China [11175224, 11121403, 31270834, 61272318, 31671369] ; National Natural Science Foundation of China [11175224, 11121403, 31270834, 61272318, 31671369]
DOIhttp://dx.doi.org/10.1186/s12859-017-1475-5
关键词[WOS]REAL-VALUE PREDICTION ; RELATIVE SOLVENT ACCESSIBILITY ; NEURAL-NETWORKS ; SECONDARY STRUCTURE ; AMINO-ACIDS ; SEQUENCE ; REGRESSION ; PROTEINS ; GENERATION ; SIMILARITY
语种英语
资助者National Basic Research Program of China [2012CB316502] ; National Basic Research Program of China [2012CB316502] ; National Natural Science Foundation of China [11175224, 11121403, 31270834, 61272318, 31671369] ; National Natural Science Foundation of China [11175224, 11121403, 31270834, 61272318, 31671369] ; National Basic Research Program of China [2012CB316502] ; National Basic Research Program of China [2012CB316502] ; National Natural Science Foundation of China [11175224, 11121403, 31270834, 61272318, 31671369] ; National Natural Science Foundation of China [11175224, 11121403, 31270834, 61272318, 31671369]
WOS类目Biochemical Research Methods ; Biotechnology & Applied Microbiology ; Mathematical & Computational Biology
引用统计
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/22106
专题2017年知识产出
通讯作者Bu, DB (reprint author), Chinese Acad Sci, Inst Comp Technol, Key Lab Intelligent Proc, Beijing 100190, Peoples R China.; Zheng, WM (reprint author), Chinese Acad Sci, Inst Theoret Phys, Beijing 100190, Peoples R China.
推荐引用方式
GB/T 7714
Gong, HE,Zhang, HC,Zhu, JW,et al. Improving prediction of burial state of residues by exploiting correlation among residues[J]. BMC BIOINFORMATICS,2017,18:70.
APA Gong, HE.,Zhang, HC.,Zhu, JW.,Wang, C.,Sun, SW.,...&Zheng, WM .(2017).Improving prediction of burial state of residues by exploiting correlation among residues.BMC BIOINFORMATICS,18,70.
MLA Gong, HE,et al."Improving prediction of burial state of residues by exploiting correlation among residues".BMC BIOINFORMATICS 18(2017):70.
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