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PEDS Advance Access originally published online on July 14, 2006
Protein Engineering Design and Selection 2006 19(9):431-437; doi:10.1093/protein/gzl027
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oxfordjournals.org

The effect of experimental resolution on the performance of knowledge-based discriminatory functions for protein structure selection

Tianyun Liu and Ram Samudrala1

Department of Microbiology, University of Washington, School of Medicine Seattle, WA 98195, USA

1To whom correspondence should be addressed. E-mail: ram{at}compbio.washington.edu

The key to an accurate method of protein structure prediction is the development of an effective discriminatory function. Knowledge-based discriminatory functions extract parameters from statistical analysis of experimentally determined protein structures. We assess how the quality of the protein structures used for compiling statistics affects the performance of a residue-specific all-atom probability discriminatory function (RAPDF). We find that the discriminatory power correlates with the quality of the structural dataset on which the RAPDF is parameterized in a statistically significant manner. The overrepresentation of unfavorable contacts in the low-resolution and NMR structures contributes to the major errors in the compilation of the conditional probabilities. Such errors weaken the discriminatory power of the function, especially when decoy conformations also contain considerable numbers of unfavorable contacts. This indicates that using high-resolution structural datasets after filtering out unfavorable contacts can improve the performance of knowledge-based discriminatory functions.

Keywords: all-atom probability discriminatory function/experimental resolution/decoy discrimination

Received February 2, 2006; revised April 21, 2006; accepted April 30, 2006.


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