Energy Functions that Discriminate X-ray and Near-native Folds from Well-constructed Decoys

摘要: This study generates ensembles of decoy or test structures for eight small proteins with a variety different folds. Between 35,000 and 200,000 decoys were generated each protein using our four-state off-lattice model together novel relaxation method. These give compact self-avoiding conformations constrained to have native secondary structure. Ensembles these used the ability several types empirical contact, surface area distance-dependent energy functions distinguish between correct incorrect conformations. tests shown that none is able consistently either X-ray conformation near-native from others which are incorrect. Certain combinations two able, however, identify amongst same better also at identifying conformations, finding them hundred-fold higher frequency than chance. The fact combination perform generally accepted suggests their future use in folding simulations perhaps threading predictions.