A method for evaluating the structural quality of protein models by using higher-order φ–ψ pairs scoring

doi:10.1073/pnas.0511333103

A method for evaluating the structural quality of protein models by using higher-order φ–ψ pairs scoring

Gregory E. Sims^† and
Sung-Hou Kim^†,^‡,^§

^†Berkeley Structural Genomics Center, Lawrence Berkeley National Laboratory, Berkeley, CA 94720; and
^‡Department of Chemistry, University of California, Berkeley, CA 94720

Contributed by Sung-Hou Kim, January 24, 2006

Abstract

A method is presented for scoring the model quality of experimental and theoretical protein structures. The structural model to be evaluated is dissected into small fragments via a sliding window, where each fragment is represented by a vector of multiple φ–ψ angles. The sliding window ranges in size from a length of 1–10 φ–ψ pairs (3–12 residues). In this method, the conformation of each fragment is scored based on the fit of multiple φ–ψ angles of the fragment to a database of multiple φ–ψ angles from high-resolution x-ray crystal structures. We show that measuring the fit of predicted structural models to the allowed conformational space of longer fragments is a significant discriminator for model quality. Reasonable models have higher-order φ–ψ score fit values (m) > −1.00.

Footnotes

^§To whom correspondence should be addressed. E-mail: shkim{at}lbl.gov
Author contributions: G.E.S. and S.-H.K. designed research; G.E.S. and S.-H.K. performed research; G.E.S. contributed new reagents/analytic tools; G.E.S. and S.-H.K. analyzed data; and G.E.S. and S.-H.K. wrote the paper.
Conflict of interest statement: No conflicts declared.
Abbreviations:

HOPP,

higher-order φ–ψ;

CASP,

Critical Assessment of Protein Structure Prediction;

GDT-TS,

global distance test total score.
Freely available online through the PNAS open access option.