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Assembling novel protein folds from super‐secondary structural fragments
Author(s) -
Jones David T.,
McGuffin Liam J.
Publication year - 2003
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.10542
Subject(s) - casp , protein structure prediction , fragment (logic) , computer science , fold (higher order function) , protein structure , computational biology , structural alignment , biological system , simulated annealing , algorithm , chemistry , biology , sequence alignment , peptide sequence , biochemistry , gene , programming language
The results of applying a fragment‐based protein tertiary structure prediction method to the prediction of 14 CASP5 target domains are described. The method is based on the assembly of supersecondary structural fragments taken from highly resolved protein structures using a simulated annealing algorithm. A number of good predictions for proteins with novel folds were produced, although not always as the first model. For two fold recognition targets, FRAGFOLD produced the most accurate model in both cases, despite the fact that the predictions were not based on a template structure. Although clear progress has been made in improving FRAGFOLD since CASP4, the ranking of final models still seems to be the main problem that needs to be addressed before the next CASP experiment. Proteins 2003;53:480–485. © 2003 Wiley‐Liss, Inc.