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BMC Bioinformatics. 2017 Mar 14;18(Suppl 3):70. doi: 10.1186/s12859-017-1475-5.

Improving prediction of burial state of residues by exploiting correlation among residues.

Gong H1,2, Zhang H1,2, Zhu J1,2, Wang C1,2, Sun S1, Zheng WM3, Bu D4.

Author information

1
Key Lab of Intelligent Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.
2
School of Computer Science, University of Chinese Academy of Sciences, Beijing, China.
3
Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, 100190, China. zheng@itp.ac.cn.
4
Key Lab of Intelligent Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China. dbu@ict.ac.cn.

Abstract

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.

KEYWORDS:

Burial states of residue; Conditional random field; Protein structure; Residue correlation

PMID:
28361691
PMCID:
PMC5374591
DOI:
10.1186/s12859-017-1475-5
[Indexed for MEDLINE]
Free PMC Article

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