Yue K, Dill K A
Department of Pharmaceutical Chemistry, University of California at San Francisco, 94143, USA.
Protein Sci. 1996 Feb;5(2):254-61. doi: 10.1002/pro.5560050209.
We describe a computer algorithm for predicting the three-dimensional structures of proteins using only their amino acid sequences. The method differs from others in two ways: (1) it uses very few energy parameters, representing hydrophobic and polar interactions, and (2) it uses a new "constraint-based exhaustive" searching method, which appears to be among the fastest and most complete search methods yet available for realistic protein models. It finds a relatively small number of low-energy conformations, among which are native-like conformations, for crambin (1CRN), avian pancreatic polypeptide (1PPT), melittin (2MLT), and apamin. Thus, the lowest-energy states of very simple energy functions may predict the native structures of globular proteins.
我们描述了一种仅使用氨基酸序列来预测蛋白质三维结构的计算机算法。该方法在两个方面与其他方法不同：（1）它仅使用很少的能量参数来表示疏水和极性相互作用；（2）它使用了一种新的“基于约束的穷举”搜索方法，这似乎是目前可用于实际蛋白质模型的最快且最全面的搜索方法之一。对于胰凝乳蛋白酶原（1CRN）、禽胰多肽（1PPT）、蜂毒肽（2MLT）和蜂毒明肽，它找到了相对较少数量的低能量构象，其中包括类似天然状态的构象。因此，非常简单的能量函数的最低能量状态可能预测球状蛋白质的天然结构。
