a pairwise residue contact area-based mean force potential for discrimination of native protein structure成对渣接触成立意味着迫使潜在的歧视本机蛋白质结构.pdfVIP

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a pairwise residue contact area-based mean force potential for discrimination of native protein structure成对渣接触成立意味着迫使潜在的歧视本机蛋白质结构.pdf

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a pairwise residue contact area-based mean force potential for discrimination of native protein structure成对渣接触成立意味着迫使潜在的歧视本机蛋白质结构

Arab et al. BMC Bioinformatics 2010, 11:16 /1471-2105/11/16 RESEARCH ARTICLE Open Access A pairwise residue contact area-based mean force potential for discrimination of native protein structure 1 2,3* 4 5 1 Shahriar Arab , Mehdi Sadeghi , Changiz Eslahchi , Hamid Pezeshk , Armita Sheari 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 Background bonds, angles and dihedral angle terms [11-14]. In addi- Considering energy function to