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Applying Undertaker to quality assessment
Author(s) -
Archie John G.,
Paluszewski Martin,
Karplus Kevin
Publication year - 2009
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.22508
Subject(s) - ranking (information retrieval) , function (biology) , computer science , quality (philosophy) , trustworthiness , data mining , artificial intelligence , mathematics , machine learning , biology , physics , computer security , quantum mechanics , evolutionary biology
Our group tested three quality assessment functions in CASP8: a function which used only distance constraints derived from alignments (SAM‐T08‐MQAO), a function which added other single‐model terms to the distance constraints (SAM‐T08‐MQAU), and a function which used both single‐model and consensus terms (SAM‐T08‐MQAC). We analyzed the functions both for ranking models for a single target and for producing an accurate estimate of GDT_TS. Our functions were optimized for the ranking problem, so are perhaps more appropriate for metaserver applications than for providing trustworthiness estimates for single models. On the CASP8 test, the functions with more terms performed better. The MQAC consensus method was substantially better than either single‐model function, and the MQAU function was substantially better than the MQAO function that used only constraints from alignments. Proteins 2009. © 2009 Wiley‐Liss, Inc.