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A method for protein accessibility prediction based on residue types and conformational states |
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| Authors: | Zarei Roghayeh Arab Shahriar Sadeghi Mehdi |
| Affiliation: | aKhatam University, Tehran, Iran bDepartment of Bioinformatics, Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran cNational Institute of Genetic Engineering and Biotechnology, Tehran, Iran dSchool of Computer Science, Institute for Studies in Theoretical Physics and Mathematics (IPM), Tehran, Iran |
| Abstract: | Prediction of protein accessibility from sequence, as prediction of protein secondary structure is an intermediate step for predicting structures and consequently functions of proteins. Most of the currently used methods are based on single residue prediction, either by statistical means or evolutionary information, and accessibility state of central residue in a window predicted. By expansion of databases of proteins with known 3D structures, we extracted information of pairwise residue types and conformational states of pairs simultaneously. For solving the problem of ambiguity in state prediction by one residue window sliding, we used dynamic programming algorithm to find the path with maximum score. The three state overall per-residue accuracy, Q3, of this method in a Jackknife test with dataset of known proteins is more than 65% which is an improvement on results of methods based on evolutionary information. |
| Keywords: | Protein structure prediction Protein accessibility prediction Information theory Dynamic programming algorithm |
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