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Open Access Highly Accessed Research article

Improving consensus contact prediction via server correlation reduction

Xin Gao1, Dongbo Bu12, Jinbo Xu3 and Ming Li1*

Author Affiliations

1 David R. Cheriton School of Computer Science, University of Waterloo, N2L3G1, Canada

2 Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100080, PR China

3 Toyota Technological Institute at Chicago, 1427 East 60th Street, Chicago, Illinois 60637, USA

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BMC Structural Biology 2009, 9:28  doi:10.1186/1472-6807-9-28

Published: 6 May 2009

Abstract

Background

Protein inter-residue contacts play a crucial role in the determination and prediction of protein structures. Previous studies on contact prediction indicate that although template-based consensus methods outperform sequence-based methods on targets with typical templates, such consensus methods perform poorly on new fold targets. However, we find out that even for new fold targets, the models generated by threading programs can contain many true contacts. The challenge is how to identify them.

Results

In this paper, we develop an integer linear programming model for consensus contact prediction. In contrast to the simple majority voting method assuming that all the individual servers are equally important and independent, the newly developed method evaluates their correlation by using maximum likelihood estimation and extracts independent latent servers from them by using principal component analysis. An integer linear programming method is then applied to assign a weight to each latent server to maximize the difference between true contacts and false ones. The proposed method is tested on the CASP7 data set. If the top L/5 predicted contacts are evaluated where L is the protein size, the average accuracy is 73%, which is much higher than that of any previously reported study. Moreover, if only the 15 new fold CASP7 targets are considered, our method achieves an average accuracy of 37%, which is much better than that of the majority voting method, SVM-LOMETS, SVM-SEQ, and SAM-T06. These methods demonstrate an average accuracy of 13.0%, 10.8%, 25.8% and 21.2%, respectively.

Conclusion

Reducing server correlation and optimally combining independent latent servers show a significant improvement over the traditional consensus methods. This approach can hopefully provide a powerful tool for protein structure refinement and prediction use.