Identification of the Protein Native Structure by Using a Sequence-Dependent Feature in Contact Maps

We present a new approach for fold recognition to identify the native and the near-native protein structures among decoy structures by using pair-wise contact potentials between amino acid residues. For a given protein structure, a new scoring function is defined as the difference between the contact energy for its native sequence and the average contact energy for random sequences of the same contact map. We have tested the new scoring function for the various decoy sets available in the literature and have found that the new scoring function is more useful than the original contact energy, especially for decoy sets where the total number of contacts from the native structure is similar to those from the decoy conformations. From this observation, we conclude that the more native-like the structure is, the more likely that it distinguishes the native sequence from random sequences. We demonstrate that, for a given contact potential, a simple, but more efficient, new scoring function can be constructed.