Predicted residue–residue contacts can help the scoring of 3D models

Abstract

During the 7th Critical Assessment of Protein Structure Prediction (CASP7) experiment, it was suggested that the real value of predicted residue-residue contacts might lie in the scoring of 3D model structures. Here, we have carried out a detailed reassessment of the contact predictions made during the recent CASP8 experiment to determine whether predicted contacts might aid in the selection of close-to-native structures or be a useful tool for scoring 3D structural models. We used the contacts predicted by the CASP8 residue-residue contact prediction groups to select models for each target domain submitted to the experiment. We found that the information contained in the predicted residue-residue contacts would probably have helped in the selection of 3D models in the free modeling regime and over the harder comparative modeling targets. Indeed, in many cases, the models selected using just the predicted contacts had better GDT-TS scores than all but the best 3D prediction groups. Despite the well-known low accuracy of residue-residue contact predictions, it is clear that the predictive power of contacts can be useful in 3D model prediction strategies.