title: A distance-dependent atomic knowledge-based potential and force for discrimination of native structures from decoys.
abstract: The purpose of this article is to introduce a novel model for discriminating correctly folded proteins from well designed decoy structures using mechanical interatomic forces. In our model, we consider a protein as a collection of springs and the force imposed to each atom is calculated. A potential function is obtained from statistical contact preferences within known protein structures. Combining this function with the spring equation, the interatomic forces are calculated. Finally, we consider a structure and define a score function on the 3D structure of a protein. We compare the force imposed to each atom of a protein with the corresponding atom in the other structures. We then assign larger scores to those atoms with lower forces. The total score is the sum of partial scores of atoms. The optimal structure is assumed to be the one with the highest score in the data set. To evaluate the performance of our model, we apply it on several decoy sets.
authors.affiliation: Department of Mathematical Sciences, Shahid Beheshti University, Post Code 1983963113, Tehran, Iran.
authors.forename: Mehdi
authors.initials: M
authors.lastname: Mirzaie
authors.forename: Changiz
authors.initials: C
authors.lastname: Eslahchi
authors.forename: Hamid
authors.initials: H
authors.lastname: Pezeshk
authors.forename: Mehdi
authors.initials: M
authors.lastname: Sadeghi
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D018709:Statistics, Nonparametric
chemical_list: D011506:Proteins