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BMC Structural Biology

, 11:38

First Online: 12 October 2011Received: 30 June 2011Accepted: 12 October 2011

Abstract

BackgroundProtein 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.

ResultsWe 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.

ConclusionsWhen 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.

Electronic supplementary materialThe online version of this article doi:10.1186-1472-6807-11-38 contains supplementary material, which is available to authorized users.

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Autor: Jesse Eickholt - Zheng Wang - Jianlin Cheng

Fuente: https://link.springer.com/



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