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Assessment of predictions submitted for the CASP7 function prediction category
Author(s) -
López Gonzalo,
Rojas Ana,
Tress Michael,
Valencia Alfonso
Publication year - 2007
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.21651
Subject(s) - casp , ontology , gene ontology , function (biology) , computer science , a priori and a posteriori , data mining , artificial intelligence , natural language processing , protein structure prediction , protein structure , gene , chemistry , epistemology , biology , biochemistry , philosophy , gene expression , evolutionary biology
Here we present a full overview of the Critical Assessment of Protein Structure Prediction (CASP7) function prediction category. Predictions were submitted for Gene Ontology molecular function terms, Enzyme Commission numbers, and ligand binding site residues. The first two categories were difficult to assess because very little new functional information becomes available after the experiment. The majority of the known Gene Ontology terms and all the Enzyme Commission numbers were available a priori to predictors before the experiment, so prediction for these two categories was not blind. Nevertheless, for Gene Ontology terms we were able to demonstrate that some groups made better predictions than others. In the binding residue category, the predictors did not know in advance which ligands were bound and therefore blind evaluation was possible, but there were disappointingly few predictions in this category. After CASP 6 and 7 the need to organize a more effective blind function prediction category is obvious, even if it means focusing on binding site prediction as the only category that can be truly assessed in the CASP spirit. Proteins 2007. © 2007 Wiley‐Liss, Inc.