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Assembling novel protein folds from super-secondary structural fragments

Jones, DT; McGuffin, LJ; (2003) Assembling novel protein folds from super-secondary structural fragments. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS , 53 (6) 480 - 485. 10.1002/prot.10542.

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Abstract

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. (C) 2003 Wiley-Liss, Inc.

Type:Article
Title:Assembling novel protein folds from super-secondary structural fragments
Location:PACIFIC GROVE, CA
DOI:10.1002/prot.10542
Keywords:protein structure prediction, folding, simulation, novel folds, fold recognition, RECOGNITION, SEQUENCES
UCL classification:UCL > School of BEAMS > Faculty of Engineering Science > Computer Science

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