Predicting structurally conserved contacts for homologous proteins using sequence conservation filters

The prediction of intramolecular contacts has a useful application in predicting the three-dimensional structures of proteins. The accuracy of the template-based contact prediction methods depends on the quality of the template structures. To reduce the false positive predictions associated with using the entire set of template-derived contacts, we develop selection filters that use sequence conservation information to predict subsets of contacts more likely to be structurally conserved between the template and the target. The method is developed specifically for protein families with few available templates such as the G protein-coupled receptor (GPCR) family. It is validated on a test set of 342 template-target pairs from three protein families, and applied to one template-target pair from the GPCR family. We find that the filter selection method increases the accuracy of contact prediction with sufficient coverage for structure prediction.