title: Improving prediction of burial state of residues by exploiting correlation among residues.
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.
authors.affiliation: Key Lab of Intelligent Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.|School of Computer Science, University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Hai'e
authors.initials: H
authors.lastname: Gong
authors.affiliation: Key Lab of Intelligent Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.|School of Computer Science, University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Haicang
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Key Lab of Intelligent Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.|School of Computer Science, University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Jianwei
authors.initials: J
authors.lastname: Zhu
authors.affiliation: Key Lab of Intelligent Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.|School of Computer Science, University of Chinese Academy of Sciences, Beijing, China.
authors.forename: Chao
authors.initials: C
authors.lastname: Wang
authors.affiliation: Key Lab of Intelligent Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China.
authors.forename: Shiwei
authors.initials: S
authors.lastname: Sun
authors.affiliation: Institute of Theoretical Physics, Chinese Academy of Sciences, Beijing, 100190, China. zheng@itp.ac.cn.
authors.forename: Wei-Mou
authors.initials: WM
authors.lastname: Zheng
authors.affiliation: Key Lab of Intelligent Processing, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China. dbu@ict.ac.cn.
authors.forename: Dongbo
authors.initials: D
authors.lastname: Bu
mesh_terms: D016208:Databases, Factual; D057927:Hydrophobic and Hydrophilic Interactions; D008962:Models, Theoretical; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D015203:Reproducibility of Results; D012997:Solvents / Q000737:chemistry
chemical_list: D011506:Proteins; D012997:Solvents
keywords: Burial states of residue; Conditional random field; Protein structure; Residue correlation