A pairwise residue contact area-based mean force potential for discrimination of native protein structure

BMC Bioinformatics

Research Article

Armita Sheari¹  Shahriar Arab¹  Changiz Eslahchi²  Mehdi Sadeghi³  Hamid Pezeshk⁴ 

[1] Department of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran;Department of Mathematics and Center of Excellence in Algebraic and Logical Structures in Discrete Mathematics, Shahid Beheshti University, Tehran, Iran;National Institute of Genetic Engineering and Biotechnology, Tehran-Karaj Highway, Tehran, Iran;School of Computer Science, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran;School of Mathematics, Statistics and Computer Sciences, Center of Excellence in Biomathematics, College of Science, University of Tehran, Tehran, Iran;

关键词: Native Structure;    Protein Structure Prediction;    Residue Type;    Probe Radius;    Side Chain Atom;   

DOI  :  10.1186/1471-2105-11-16

 received in 2009-06-13, accepted in 2010-01-09,  发布年份 2010

来源: Springer

【 摘 要 】

BackgroundConsidering 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.ResultsWe 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.ConclusionsThis 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

【 授权许可】

Unknown   
© Arab et al; licensee BioMed Central Ltd. 2010. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.