title: DomHR: accurately identifying domain boundaries in proteins using a hinge region strategy.
abstract: BACKGROUND
  The precise prediction of protein domains, which are the structural, functional and evolutionary units of proteins, has been a research focus in recent years. Although many methods have been presented for predicting protein domains and boundaries, the accuracy of predictions could be improved.
  
  
  RESULTS
  In this study we present a novel approach, DomHR, which is an accurate predictor of protein domain boundaries based on a creative hinge region strategy. A hinge region was defined as a segment of amino acids that covers part of a domain region and a boundary region. We developed a strategy to construct profiles of domain-hinge-boundary (DHB) features generated by sequence-domain/hinge/boundary alignment against a database of known domain structures. The DHB features had three elements: normalized domain, hinge, and boundary probabilities. The DHB features were used as input to identify domain boundaries in a sequence. DomHR used a nonredundant dataset as the training set, the DHB and predicted shape string as features, and a conditional random field as the classification algorithm. In predicted hinge regions, a residue was determined to be a domain or a boundary according to a decision threshold. After decision thresholds were optimized, DomHR was evaluated by cross-validation, large-scale prediction, independent test and CASP (Critical Assessment of Techniques for Protein Structure Prediction) tests. All results confirmed that DomHR outperformed other well-established, publicly available domain boundary predictors for prediction accuracy.
  
  
  BACKGROUND
  The DomHR is available at http://cal.tongji.edu.cn/domain/.
authors.affiliation: Department of Chemistry, Tongji University, Shanghai, China.
authors.forename: Xiao-yan
authors.initials: XY
authors.lastname: Zhang
authors.forename: Long-jian
authors.initials: LJ
authors.lastname: Lu
authors.forename: Qi
authors.initials: Q
authors.lastname: Song
authors.forename: Qian-qian
authors.initials: QQ
authors.lastname: Yang
authors.forename: Da-peng
authors.initials: DP
authors.lastname: Li
authors.forename: Jiang-ming
authors.initials: JM
authors.lastname: Sun
authors.forename: Tong-hua
authors.initials: TH
authors.lastname: Li
authors.forename: Pei-sheng
authors.initials: PS
authors.lastname: Cong
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D008969:Molecular Sequence Data; D017434:Protein Structure, Tertiary / Q000235:genetics*; D011506:Proteins / Q000737:chemistry*; D040901:Proteomics / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins