A new protein representation based on fragment contacts: towards an improvement of contact maps predictions

Prediction of intramolecular residue-to-residue contacts is a difficult problem. In this paper we consider a related subproblem: the fragment-to-fragment contact prediction problem. A fragment contact map is a coarse-grained approximation of a residue contact map. Although fragment contact maps are approximations, they still contain most information about residue contacts and, most importantly, they are more tolerant to errors than contact maps (at least random error). We compare with an extensive set of experimental tests the error tolerance of fragment contact maps with respect to the error tolerance of residue contact maps. Moreover, as a simple concrete application, we show how to build a fragment contact predictor from a residue contact predictor and we show that in some cases this technique can improve contact predictions.