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Paper   IPM / Biological / 13253
School of Biological Sciences
  Title:   A Method for Protein Accessibility Prediction Based on Residue types and Conformational States
1.  R. Zarei.
2.  S. Arab.
3.  M. Sadeghi.
  Status:   Published
  Journal: Computational Biology and Chemistry
  No.:  5
  Vol.:  31
  Year:  2007
  Pages:   384-388
  Supported by:  IPM
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

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