Terwilliger Thomas C
Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Acta Crystallogr D Biol Crystallogr. 2010 Mar;66(Pt 3):285-94. doi: 10.1107/S0907444910000272. Epub 2010 Feb 12.
A method for the rapid tracing of polypeptide backbones has been developed. The method creates an approximate chain tracing that is useful for visual evaluation of whether a structure has been solved and for use in scoring the quality of electron-density maps. The essence of the method is to (i) sample candidate C(alpha) positions at spacings of approximately 0.6 A along ridgelines of high electron density, (ii) list all possible nonapeptides that satisfy simple geometric and density criteria using these candidate C(alpha) positions, (iii) score the nonapeptides and choose the highest scoring ones, and (iv) find the longest chains that can be made by connecting nonamers. An indexing and storage scheme that allows a single calculation of most distances and density values is used to speed up the process. The method was applied to 42 density-modified electron-density maps at resolutions from 1.5 to 3.8 A. A total of 21 428 residues in these maps were traced in 24 CPU min with an overall r.m.s.d. of 1.61 A for C(alpha) atoms compared with the known refined structures. The method appears to be suitable for rapid evaluation of electron-density map quality.
已开发出一种快速追踪多肽主链的方法。该方法创建了一个近似的链追踪，这对于直观评估结构是否已解析以及用于评估电子密度图的质量很有用。该方法的核心是：（i）沿着高电子密度的脊线以约0.6 Å的间距对候选Cα位置进行采样；（ii）使用这些候选Cα位置列出所有满足简单几何和密度标准的九肽；（iii）对九肽进行评分并选择得分最高的九肽；（iv）找到通过连接九肽可以形成的最长链。使用一种索引和存储方案来加速该过程，该方案允许对大多数距离和密度值进行单次计算。该方法应用于42个分辨率在1.5至3.8 Å之间的密度修正电子密度图。在24个CPU分钟内追踪了这些图中的总共21428个残基，与已知的精制结构相比，Cα原子的总体均方根偏差为1.61 Å。该方法似乎适用于快速评估电子密度图的质量。
