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Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM.

Type Information
Nr 11 (Research article)
Authors Kim, David; Chivian, Dylan; Malmström, Lars; Baker, David
Title Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM.
Journal Proteins (2005) Suppl 7 193-200
DOI 10.1002/prot.20737
Citations 114 citations (journal impact: 3.42)
Abstract Domain boundary prediction is an important step in both experimental and computational protein structure characterization. We have developed two fully automated domain parsing methods the first Ginzu which we have described previously utilizes information from homologous sequences and structures while the second RosettaDOM which has not been described previously uses only information in the query sequence. Ginzu iteratively assigns domains by homology to structures and sequence families using successively less confident methods. RosettaDOM uses the Rosetta de novo structure prediction method to build three-dimensional models and then applies Taylors structure based domain assignment method to parse the models into domains. Domain boundaries observed repeatedly in the models are predicted to be domain boundaries for the protein. Interestingly RosettaDOM produced quite good domain predictions for proteins of a size typically considered to be beyond the reach of de novo structure prediction methods. For remote fold recognition targets and new folds both Ginzu and RosettaDOM produced promising results and in some cases where one method failed to detect the correct domain boundary it was correctly identified by the other method. We describe here the successes and failures using both methods and address the possibility of incorporating both protocols into an improved hybrid method. Proteins 2005. c 2005 Wiley-Liss Inc.