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Open Access Highly Accessed Research article

A conformation ensemble approach to protein residue-residue contact

Jesse Eickholt1, Zheng Wang1 and Jianlin Cheng123*

Author Affiliations

1 Department of Computer Science, University of Missouri, Columbia, MO 65211, USA

2 Informatics Institute, University of Missouri, Columbia, MO 65211, USA

3 C. Bond Life Science Center, University of Missouri, Columbia, MO 65211, USA

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BMC Structural Biology 2011, 11:38  doi:10.1186/1472-6807-11-38

Published: 12 October 2011

Abstract

Background

Protein residue-residue contact prediction is important for protein model generation and model evaluation. Here we develop a conformation ensemble approach to improve residue-residue contact prediction. We collect a number of structural models stemming from a variety of methods and implementations. The various models capture slightly different conformations and contain complementary information which can be pooled together to capture recurrent, and therefore more likely, residue-residue contacts.

Results

We applied our conformation ensemble approach to free modeling targets from both CASP8 and CASP9. Given a diverse ensemble of models, the method is able to achieve accuracies of. 48 for the top L/5 medium range contacts and. 36 for the top L/5 long range contacts for CASP8 targets (L being the target domain length). When applied to targets from CASP9, the accuracies of the top L/5 medium and long range contact predictions were. 34 and. 30 respectively.

Conclusions

When operating on a moderately diverse ensemble of models, the conformation ensemble approach is an effective means to identify medium and long range residue-residue contacts. An immediate benefit of the method is that when tied with a scoring scheme, it can be used to successfully rank models.