Simons K T, Strauss C, Baker D
Unversity of Washington, Seattle, WA 98195, USA.
J Mol Biol. 2001 Mar 9;306(5):1191-9. doi: 10.1006/jmbi.2000.4459.
We present the results of a large-scale testing of the ROSETTA method for ab initio protein structure prediction. Models were generated for two independently generated lists of small proteins (up to 150 amino acid residues), and the results were evaluated using traditional rmsd based measures and a novel measure based on the structure-based comparison of the models to the structures in the PDB using DALI. For 111 of 136 all alpha and alpha/beta proteins 50 to 150 residues in length, the method produced at least one model within 7 A rmsd of the native structure in 1000 attempts. For 60 of these proteins, the closest structure match in the PDB to at least one of the ten most frequently generated conformations was found to be structurally related (four standard deviations above background) to the native protein. These results suggest that ab initio structure prediction approaches may soon be useful for generating low resolution models and identifying distantly related proteins with similar structures and perhaps functions for these classes of proteins on the genome scale.
我们展示了用于从头预测蛋白质结构的ROSETTA方法的大规模测试结果。针对两个独立生成的小蛋白质列表（最多150个氨基酸残基）生成了模型，并使用基于传统均方根偏差（rmsd）的方法以及一种基于使用DALI将模型与PDB中的结构进行基于结构的比较的新方法对结果进行了评估。对于136个长度为50至150个残基的全α和α/β蛋白质中的111个，该方法在1000次尝试中至少产生了一个与天然结构的均方根偏差在7埃以内的模型。对于其中60种蛋白质，发现PDB中与十个最常生成的构象中至少一个最接近的结构匹配与天然蛋白质在结构上相关（比背景高四个标准差）。这些结果表明，从头结构预测方法可能很快可用于生成低分辨率模型，并在基因组规模上识别具有相似结构甚至可能具有相似功能的远缘相关蛋白质。
