title: Evaluation of domain prediction in CASP6.
abstract: We present an analysis of the domain boundary prediction, a new category, in the sixth community-wide experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP6). There were 1011 predictions submitted for 63 targets. Each prediction was compared to the set of domains defined manually by visual inspection of the experimental structure. The comparison was scored using a new domain prediction scoring scheme. As the definition of a domain is subjective, many targets were assigned alternate definitions. For such targets, each prediction was compared with all different definitions and the best score was chosen. The predictors found it difficult to accurately predict domain boundaries when the target protein contained many domains or domains made of multiple sequence segments. The CBRC-DR (P0536) and Sternberg (P0237) groups were the most successful among human experts, while Baker-Rossettadom (P0353) and Baker-Robetta-Ginzu (P0421) did well among servers.
authors.affiliation: Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
authors.forename: Chin-Hsien
authors.initials: CH
authors.lastname: Tai
authors.affiliation: Department of Computer Science, University of Maryland, College Park, Maryland.
authors.forename: Woei-Jyh
authors.initials: WJ
authors.lastname: Lee
authors.affiliation: Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
authors.forename: James J
authors.initials: JJ
authors.lastname: Vincent
authors.affiliation: Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland.
authors.forename: Byungkook
authors.initials: B
authors.lastname: Lee
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D003201:Computers; D030562:Databases, Protein; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D040901:Proteomics / Q000379:methods*; D015203:Reproducibility of Results; D016415:Sequence Alignment; D012984:Software