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Prediction of novel and analogous folds using fragment assembly and fold recognition
Author(s) -
Jones D. T.,
Bryson K.,
Coleman A.,
McGuffin L. J.,
Sadowski M. I.,
Sodhi J. S.,
Ward J. J.
Publication year - 2005
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.20731
Subject(s) - parsing , protein structure prediction , fold (higher order function) , fragment (logic) , computer science , support vector machine , casp , artificial intelligence , protein folding , protein secondary structure , docking (animal) , pattern recognition (psychology) , computational biology , algorithm , protein structure , chemistry , biology , programming language , biochemistry , medicine , nursing
Abstract A number of new and newly improved methods for predicting protein structure developed by the Jones–University College London group were used to make predictions for the CASP6 experiment. Structures were predicted with a combination of fold recognition methods (mGenTHREADER, nFOLD, and THREADER) and a substantially enhanced version of FRAGFOLD, our fragment assembly method. Attempts at automatic domain parsing were made using DomPred and DomSSEA, which are based on a secondary structure parsing algorithm and additionally for DomPred, a simple local sequence alignment scoring function. Disorder prediction was carried out using a new SVM‐based version of DISOPRED. Attempts were also made at domain docking and “microdomain” folding in order to build complete chain models for some targets. Proteins 2005;Suppl 7:143–151. © 2005 Wiley‐Liss, Inc.