Consensus contact prediction by linear programming.

Protein inter-residue contacts are of great use for protein structure determination or prediction. Recent CASP events have shown that a few accurately predicted contacts can help improve both computational efficiency and prediction accuracy of the ab inito folding methods. This paper develops an integer linear programming (ILP) method for consensus-based contact prediction. In contrast to the simple "majority voting" method assuming that all the individual servers are equal and independent, our method evaluates their correlations using the maximum likelihood method and constructs some latent independent servers using the principal component analysis technique. Then, we use an integer linear programming model to assign weights to these latent servers in order to maximize the deviation between the correct contacts and incorrect ones; our consensus prediction server is the weighted combination of these latent servers. In addition to the consensus information, our method also uses server-independent correlated mutation (CM) as one of the prediction features. Experimental results demonstrate that our contact prediction server performs better than the "majority voting" method. The accuracy of our method for the top L/5 contacts on CASP7 targets is 73.41%, which is much higher than previously reported studies. On the 16 free modeling (FM) targets, our method achieves an accuracy of 37.21%.