Iakes Ezkurdia | PubMed Health

PubMed2005

Domain definition and target classification for CASP6.

Assessment of structure predictions in CASP6 was based on single domains isolated from experimentally determined structures, which were categorized into comparative modeling, fold recognition, and new fold targets. Domain definitions were defined upon visual examination of the structures with the aid of automated domain-parsing programs. Domain categorization was determined by comparison of the target structures with those in the Protein Data Bank at the time each target expired and a variety of sequence and structure-based methods to determine potential homologous relationships.

Amino Acid Sequence↗

PubMed2005

Assessment of predictions submitted for the CASP6 comparative modeling category.

Here we present a full overview of the Critical Assessment of Protein Structure Prediction (CASP6) comparative modeling category. Prediction accuracy for the 43 comparative modeling targets was assessed through detailed numerical comparisons between predicted and experimental structures. Assessments using standard measures for model backbone quality and structural alignment accuracy highlighted a small number of groups with stand out predictions and these findings were backed up by statistical comparisons. We were able to carry out evaluations of side-chain contacts predictions and side-chain rotamer accuracy, for which one group turned out to have statistically better predictions. We also assessed the prediction quality of structurally divergent regions and biologically important sites. Interestingly we were able to show that predictors were not predicting these important functional regions with any greater accuracy than the rest of the structure. In addition we investigated the ability of predictors to build models that improve on the structural template and reached some tentative conclusions from comparisons with the previous CASP experiment.

Algorithms↗