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A distance-dependent atomic knowledge-based potential and force for discrimination of native structures from decoys

Authors

  • Mehdi Mirzaie,

    1. Department of Mathematical Sciences, Shahid Beheshti University, Post Code 1983963113, Tehran, Iran
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  • Changiz Eslahchi,

    Corresponding author
    1. Department of Mathematical Sciences, Shahid Beheshti University, Post Code 1983963113, Tehran, Iran
    • Department of Mathematical Sciences, Shahid Beheshti University, Post Code 1983963113, Tehran, Iran
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  • Hamid Pezeshk,

    1. School of Mathematics, Statistics and Computer Science, College of Science, Center of Excellence in Biomathematics, University of Tehran, Tehran, Iran
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  • Mehdi Sadeghi

    1. School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
    2. National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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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. Proteins 2009. © 2009 Wiley-Liss, Inc.

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