title: Probabilistic expression of spatially varied amino acid dimers into general form of Chou׳s pseudo amino acid composition for protein fold recognition.
abstract: BACKGROUND
  Identification of the tertiary structure (3D structure) of a protein is a fundamental problem in biology which helps in identifying its functions. Predicting a protein׳s fold is considered to be an intermediate step for identifying the tertiary structure of a protein. Computational methods have been applied to determine a protein׳s fold by assembling information from its structural, physicochemical and/or evolutionary properties.
  
  
  METHODS
  In this study, we propose a scheme in which a feature extraction technique that extracts probabilistic expressions of amino acid dimers, which have varying degree of spatial separation in the primary sequences of proteins, from the Position Specific Scoring Matrix (PSSM). SVM classifier is used to create a model from extracted features for fold recognition.
  
  
  RESULTS
  The performance of the proposed scheme is evaluated against three benchmarked datasets, namely the Ding and Dubchak, Extended Ding and Dubchak, and Taguchi and Gromiha datasets.
  
  
  CONCLUSIONS
  The proposed scheme performed well in the experiments conducted, providing improvements over previously published results in literature.
authors.affiliation: University of the South Pacific, Fiji. Electronic address: saini_h@usp.ac.fj.
authors.forename: Harsh
authors.initials: H
authors.lastname: Saini
authors.affiliation: University of the South Pacific, Fiji. Electronic address: raicar_g@usp.ac.fj.
authors.forename: Gaurav
authors.initials: G
authors.lastname: Raicar
authors.affiliation: University of the South Pacific, Fiji; Griffith University, Brisbane, Australia. Electronic address: sharma_al@usp.ac.fj.
authors.forename: Alok
authors.initials: A
authors.lastname: Sharma
authors.affiliation: University of the South Pacific, Fiji. Electronic address: lal_s@usp.ac.fj.
authors.forename: Sunil
authors.initials: S
authors.lastname: Lal
authors.affiliation: Griffith University, Brisbane, Australia. Electronic address: a.dehzangi@griffith.edu.au.
authors.forename: Abdollah
authors.initials: A
authors.lastname: Dehzangi
authors.affiliation: Griffith University, Brisbane, Australia. Electronic address: james.lyons@griffithuni.edu.au.
authors.forename: James
authors.initials: J
authors.lastname: Lyons
authors.affiliation: Griffith University, Brisbane, Australia. Electronic address: k.paliwal@griffith.edu.au.
authors.forename: Kuldip K
authors.initials: KK
authors.lastname: Paliwal
authors.affiliation: Human Genome Center, University of Tokyo, Japan. Electronic address: imoto@ims.u-tokyo.ac.jp.
authors.forename: Seiya
authors.initials: S
authors.lastname: Imoto
authors.affiliation: Human Genome Center, University of Tokyo, Japan. Electronic address: miyano@hgc.jp.
authors.forename: Satoru
authors.initials: S
authors.lastname: Miyano
mesh_terms: D000596:Amino Acids / Q000737:chemistry*; D001665:Binding Sites; D066264:Datasets as Topic; D019281:Dimerization; D011336:Probability; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
chemical_list: D000596:Amino Acids; D011506:Proteins