Potential energy function for continuous state models of globular proteins.
Potential energy function for continuous state models of globular proteins.
复制标题
球状蛋白连续状态模型的势能函数。
DOI：
10.1089/106652700750050835
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发表时间：
2000
期刊：
影响因子：
--
通讯作者：
Crippen,GM
中科院分区：
文献类型：
--
作者：
Ohkubo,YZ;Crippen,GM
蛋白质结构预测的方法之一是获得能量函数，该能量函数可以在一系列构象中识别给定序列的天然构象。这些区分可以通过将最低能量分配给原生构象来完成，同时保证原生构象在动物园中。因此，调整得很好的函数可以用于搜索其他(接近)原住民。这里的目的是通过成对的能量势在相对较高的分辨率(本地和最接近的非本地之间的RMSD差约为1？)下进行区分。这种潜力是用实验确定的只有一种蛋白质的天然构象来训练的，而不是通常对许多蛋白质进行的大规模调查。新颖的特征是，将天然结构与更广泛和更具挑战性的非天然结构阵列进行比较，不仅通过通常的穿线过程，而且通过广泛的局部最小化潜力来发现。由于这种极其苛刻的搜索，原生函数非常接近势函数的明显全局最小值。对于另一种具有60%序列同一性的蛋白质来说，全局最低属性是成立的，但它在完全不同的蛋白质上的表现当然要弱得多。
One of the approaches to protein structure prediction is to obtain energy functions which can recognize the native conformation of a given sequence among a zoo of conformations. The discriminations can be done by assigning the lowest energy to the native conformation, with the guarantee that the native is in the zoo. Well-adjusted functions, then, can be used in the search for other (near-) natives. Here the aim is the discrimination at relatively high resolution (RMSD difference between the native and the closest nonnative is around 1 Å) by pairwise energy potentials. The potential is trained using the experimentally determined native conformation of only one protein, instead of the usual large survey over many proteins. The novel feature is that the native structure is compared to a vastly wider and more challenging array of nonnative structures found not only by the usual threading procedure, but by wide-ranging local minimization of the potential. Because of this extremely demanding search, the native is very close to the apparent global minimum of the potential function. The global minimum property holds up for one other protein having 60% sequence identity, but its performance on completely dissimilar proteins is of course much weaker.