Factors affecting the ability of energy functions to discriminate correct from incorrect folds
Factors affecting the ability of energy functions to discriminate correct from incorrect folds
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DOI：
10.1006/jmbi.1996.0809
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发表时间：
1997-03-07
影响因子：
5.6
通讯作者：
Levitt, M
中科院分区：
文献类型：
--
作者：
Park, BH;Huang, ES;Levitt, M
测试了十八个低和中分辨率经验能量函数从三个诱饵蛋白构象测试集中区分正确和错误折叠的能力。能量函数包括 13 个成对的平均力势，涵盖了广泛的函数形式和参数化方法，尝试检测正确形成的疏水核心的四种势，以及一种基于环境的势。三个测试集中的第一个由八个小蛋白质的合理构象的大集合组成，所有这些都具有正确的天然二级结构并且相当紧凑。第二个是已知蛋白质结构数据库中所有子构象的集合，应用于该数据库中的序列（无间隙线程）。第三个是一组由 1000 个构象组成的集合，每个构象对应于 7 个小蛋白质，取自 298 K 和 498 K 的分子动力学模拟。我们的结果表明，每个挑战集都有有效的函数；此外，一项测试的成功并不能保证另一项测试的成功。我们检查了对于准确区分每个测试集中的正确结构似乎很重要的因素，并注意到极其简单的函数通常与更复杂的函数一样有效。 (C) 1997 学术出版社有限公司。
Eighteen low and medium resolution empirical energy functions were tested for their ability to distinguish correct from incorrect folds from three test sets of decoy protein conformations. The energy functions included 13 pairwise potentials of mean force, covering a wide range of functional forms and methods of parameterization, four potentials that attempt to detect properly formed hydrophobic cores, and one environment-based potential. The first of the three test sets consists of large ensembles of plausible conformations for eight small proteins, all of which have correct native secondary structure and are reasonably compact. The second is the set of all subconformations in a database of known protein structures applied to the sequences in that database (ungapped threading). The third is a set of ensembles of 1000 conformations each for seven small proteins taken from molecular dynamics simulations at 298 K and 498 K. Our results show that there are functions effective for each challenge set; moreover, success in one test is no guarantee of success in another. We examine the factors that seem to be important for accurate discrimination of correct structures in each of the test sets, and note that extremely simple functions are often as effective as more complex functions. (C) 1997 Academic Press Limited.