Applying undertaker cost functions to model quality assessment
Article first published online: 30 SEP 2008
Copyright © 2008 Wiley-Liss, Inc.
Proteins: Structure, Function, and Bioinformatics
Volume 75, Issue 3, pages 550–555, 15 May 2009
How to Cite
Archie, J. and Karplus, K. (2009), Applying undertaker cost functions to model quality assessment. Proteins, 75: 550–555. doi: 10.1002/prot.22288
- Issue published online: 24 MAR 2009
- Article first published online: 30 SEP 2008
- Accepted manuscript online: 30 SEP 2008 12:00AM EST
- Manuscript Accepted: 16 SEP 2008
- Manuscript Revised: 5 SEP 2008
- Manuscript Received: 25 APR 2008
- NIH. Grant Numbers: R01GM068570, T32GM070386
- quality assessment;
Undertaker is a program designed to help predict protein structure using alignments to proteins of known structure and fragment assembly. The program generates conformations and uses cost functions to select the best structures from among the generated conformations. This paper describes the use of Undertaker's cost functions for model quality assessment. We achieve an accuracy that is similar to other methods, without using consensus-based techniques. Adding consensus-based features further improves our approach substantially. We report several correlation measures, including a new weighted version of Kendall's τ (τ3) and show model quality assessment results superior to previously published results on all correlation measures when using only models with no missing atoms. Proteins 2009. © 2008 Wiley-Liss, Inc.