Energy functions that discriminate X-ray and near-native folds from well-constructed decoys
Energy functions that discriminate X-ray and near-native folds from well-constructed decoys
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DOI：
10.1006/jmbi.1996.0256
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发表时间：
1996-05-03
影响因子：
5.6
通讯作者：
Levitt, M
中科院分区：
文献类型：
--
作者：
Park, B;Levitt, M
这项研究为8种具有不同折叠方式的小蛋白质生成了诱饵（假目标）或测试结构集合。使用我们的四态非格点模型以及一种新的松弛方法，为每种蛋白质生成了35000到200000个诱饵。这些诱饵都具有紧凑的自回避构象，并且都被限制具有天然的二级结构。利用这些诱饵构象的集合来测试几种类型的经验性接触、表面积以及距离相关的能量函数区分正确构象和错误构象的能力。这些测试表明，这些函数中没有一个能够始终如一地将X射线构象或接近天然的构象与其他错误构象区分开来。然而，其中两种能量函数的某些组合能够始终从诱饵构象中识别出X射线结构。同样的这些组合在识别接近天然的构象方面也更好，识别出它们的频率始终比随机情况高100倍。这些组合能量函数比普遍接受的能量函数表现更好这一事实表明它们在未来的折叠模拟以及可能的穿线预测中的应用前景。（C）1996年学术出版社有限公司
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. (C) 1996 Academic Press Limited