Fidelis K, Stern P S, Bacon D, Moult J
Center for Advanced Research in Biotechnology, University of Maryland, Rockville 20850.
Protein Eng. 1994 Aug;7(8):953-60. doi: 10.1093/protein/7.8.953.
Two principal methods of determining the conformation of short pieces of polypeptide backbone in proteins have been developed: using a database of known structures and systematically generating all conformations. In this paper, we compare the effectiveness of these two techniques. The completeness of the database for segments of different lengths is examined and it is found to contain most conformations for segments seven residues long, but to deteriorate rapidly for longer regions. When the database segment is to be incorporated into the rest of a structure, at least seven residues are required to build four new residues, because of the need to position the segment relative to the rest of the structure. It is found that such positioning using flanking residues results in large errors in the inserted region. We conclude that the database method is currently not effective for comparative modeling, even for short segments. The systematic search procedure is found to generate almost all structures of short segments found in proteins. In contrast to the database method, low root mean square error structures are obtained for a set of trial segments embedded in the rest of a protein structure. Thus, it should be considered the method of choice.
使用已知结构数据库并系统地生成所有构象。在本文中，我们比较了这两种技术的有效性。研究了不同长度片段数据库的完整性，发现它包含了大多数七个残基长片段的构象，但对于更长的区域，其完整性迅速下降。当将数据库片段并入结构的其余部分时，由于需要将片段相对于结构的其余部分进行定位，构建四个新残基至少需要七个残基。发现使用侧翼残基进行这种定位会在插入区域产生较大误差。我们得出结论，即使对于短片段，数据库方法目前对于比较建模也无效。发现系统搜索程序几乎可以生成蛋白质中发现的短片段的所有结构。与数据库方法相反，对于嵌入蛋白质结构其余部分的一组试验片段，获得了低均方根误差结构。因此，它应该被视为首选方法。
