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Prediction of protein secondary structure based on residue pair types and conformational states using dynamic programming algorithm
Author(s) -
Sadeghi Mehdi,
Parto Sahar,
Arab Shahriar,
Ranjbar Bijan
Publication year - 2005
Publication title -
febs letters
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.593
H-Index - 257
eISSN - 1873-3468
pISSN - 0014-5793
DOI - 10.1016/j.febslet.2005.04.082
Subject(s) - jackknife resampling , pairwise comparison , residue (chemistry) , algorithm , dynamic programming , sliding window protocol , protein secondary structure , ambiguity , computer science , mathematics , biological system , chemistry , artificial intelligence , statistics , biology , biochemistry , estimator , window (computing) , programming language , operating system
We have used a statistical approach for protein secondary structure prediction based on information theory and simultaneously taking into consideration pairwise residue types and conformational states. Since the prediction of residue secondary structure by one residue window sliding make ambiguity in state prediction, we used a dynamic programming algorithm to find the path with maximum score. A score system for residue pairs in particular conformations is derived for adjacent neighbors up to ten residue apart in sequence. The three state overall per‐residue accuracy, Q 3 , of this method in a jackknife test with dataset created from PDBSELECT is more than 70%.