Samudrala R, Moult J
Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, Rockville 20850, USA.
Protein Eng. 1998 Nov;11(11):991-7. doi: 10.1093/protein/11.11.991.
A discriminatory function based on a statistical analysis of atomic contacts in protein structures is used for selecting side chain rotamers given a peptide main chain. The function allows us to rank different possible side chain conformations on the basis of contacts between side chain atoms and atoms in the environment. We compare the differences in constructing side chain conformations using contacts with only the local main chain, using the entire main chain, and by building pairs of side chains simultaneously with local main chain information. Using only the local main chain allows us to construct side chains with approximately 75% of the chi1 angles within 30 degrees of the experimental value, and an average side chain atom r.m.s.d. of 1.72 A in a set of 10 proteins. The results of constructing side chains for the 10 proteins are compared with the results of other side chain building methods previously published. The comparison shows similar accuracies. An advantage of the present method is that it can be used to select a small number of likely side chain conformations for each residue, thus permitting limited combinatorial searches for building multiple protein side chains simultaneously.
基于对蛋白质结构中原子接触进行统计分析的判别函数，用于在给定肽主链的情况下选择侧链旋转异构体。该函数使我们能够根据侧链原子与周围环境中原子之间的接触，对不同的可能侧链构象进行排序。我们比较了仅使用局部主链的接触、使用整个主链的接触以及结合局部主链信息同时构建侧链对来构建侧链构象时的差异。仅使用局部主链时，在一组10种蛋白质中，我们能够构建出约75%的χ1角在实验值30度范围内的侧链，且侧链原子的平均均方根偏差为1.72 Å。将这10种蛋白质构建侧链的结果与先前发表的其他侧链构建方法的结果进行了比较。比较结果显示准确性相似。本方法的一个优点是，它可用于为每个残基选择少量可能的侧链构象，从而允许进行有限的组合搜索以同时构建多个蛋白质侧链。
