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Applying Undertaker to quality assessment.

Authors
  • Archie, John G1
  • Paluszewski, Martin
  • Karplus, Kevin
  • 1 Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.
Type
Published Article
Journal
Proteins Structure Function and Bioinformatics
Publisher
Wiley (John Wiley & Sons)
Publication Date
2009
Volume
77 Suppl 9
Pages
191–195
Identifiers
DOI: 10.1002/prot.22508
PMID: 19639637
Source
Medline
License
Unknown

Abstract

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.

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