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Energy functions that discriminate X-ray and near native folds from well-constructed decoys - PubMed

  • ️Mon Jan 01 1996

. 1996 May 3;258(2):367-92.

doi: 10.1006/jmbi.1996.0256.

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Energy functions that discriminate X-ray and near native folds from well-constructed decoys

B Park et al. J Mol Biol. 1996.

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Abstract

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

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