title: A pairwise residue contact area-based mean force potential for discrimination of native protein structure.
abstract: BACKGROUND
  Considering energy function to detect a correct protein fold from incorrect ones is very important for protein structure prediction and protein folding. Knowledge-based mean force potentials are certainly the most popular type of interaction function for protein threading. They are derived from statistical analyses of interacting groups in experimentally determined protein structures. These potentials are developed at the atom or the amino acid level. Based on orientation dependent contact area, a new type of knowledge-based mean force potential has been developed.
  
  
  RESULTS
  We developed a new approach to calculate a knowledge-based potential of mean-force, using pairwise residue contact area. To test the performance of our approach, we performed it on several decoy sets to measure its ability to discriminate native structure from decoys. This potential has been able to distinguish native structures from the decoys in the most cases. Further, the calculated Z-scores were quite high for all protein datasets.
  
  
  CONCLUSIONS
  This knowledge-based potential of mean force can be used in protein structure prediction, fold recognition, comparative modelling and molecular recognition. The program is available at http://www.bioinf.cs.ipm.ac.ir/softwares/surfield.
authors.affiliation: Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
authors.forename: Shahriar
authors.initials: S
authors.lastname: Arab
authors.forename: Mehdi
authors.initials: M
authors.lastname: Sadeghi
authors.forename: Changiz
authors.initials: C
authors.lastname: Eslahchi
authors.forename: Hamid
authors.initials: H
authors.lastname: Pezeshk
authors.forename: Armita
authors.initials: A
authors.lastname: Sheari
mesh_terms: D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*
chemical_list: D011506:Proteins