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A method for evaluating the structural quality of protein models by using higher-order phi-psi pairs scoring.

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 phi-psi angles. The sliding window ranges in size from a length of 1-10 phi-psi pairs (3-12 residues). In this method, the conformation of each fragment is scored based on the fit of multiple phi-psi angles of the fragment to a database of multiple phi-psi 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 phi-psi score fit values (m) > -1.00.

SUBMITTER: Sims GE

PROVIDER: S-EPMC1401231 | biostudies-literature | 2006 Mar

REPOSITORIES: biostudies-literature

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A method for evaluating the structural quality of protein models by using higher-order phi-psi pairs scoring.

Sims Gregory E GE Kim Sung-Hou SH

Proceedings of the National Academy of Sciences of the United States of America 20060314 12

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 phi-psi angles. The sliding window ranges in size from a length of 1-10 phi-psi pairs (3-12 residues). In this method, the conformation of each fragment is scored based on the fit of multiple phi-psi angles of the fragment to a database of mult ...[more]

PMID: 16537409

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