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Bioinformatics Advance Access originally published online on March 25, 2009
Bioinformatics 2009 25(10):1259-1263; doi:10.1093/bioinformatics/btp148
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Structure similarity measure with penalty for close non-equivalent residues

Ruslan I. Sadreyev 1, ShuoYong Shi 2, David Baker 3 and Nick V. Grishin 1,2,*

1Howard Hughes Medical Institute, 2Department of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9050 and 3Department of Biochemistry, University of Washington, J Wing, Health Sciences Building, Box 357350, Seattle, WA 98195, USA

*To whom correspondence should be addressed.


  Abstract

Motivation:Recent improvement in homology-based structure modeling emphasizes the importance of sensitive evaluation measures that help identify and correct modest distortions in models compared with the target structures. Global Distance Test Total Score (GDT_TS), otherwise a very powerful and effective measure for model evaluation, is still insensitive to and can even reward such distortions, as observed for remote homology modeling in the latest CASP8 (Comparative Assessment of Structure Prediction).

Results:We develop a new measure that balances GDT_TS reward for the closeness of equivalent model and target residues (‘attraction’ term) with the penalty for the closeness of non-equivalent residues (‘repulsion’ term). Compared with GDT_TS, the resulting score, TR (total score with repulsion), is much more sensitive to structure compression both in real remote homologs and in CASP models. TR is correlated yet different from other measures of structure similarity. The largest difference from GDT_TS is observed in models of mid-range quality based on remote homology modeling.

Availability:The script for TR calculation is included in Supplementary Material. TR scores for all server models in CASP8 are available at http://prodata.swmed.edu/CASP8.

Contact: grishin{at}chop.swmed.edu

Supplementary information:All scripts and numerical data are available for download at ftp://iole.swmed.edu/pub/tr_score/

Associate Editor: Burkhard Rost

Received on January 21, 2009; revised on March 11, 2009; accepted on March 12, 2009

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