The importance of alignment accuracy for molecular replacement
The importance of alignment accuracy for molecular replacement
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DOI：
10.1107/s0907444904010145
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发表时间：
2004-07-01
影响因子：
2.2
通讯作者：
Jaroszewski, L
中科院分区：
文献类型：
--
作者：
Schwarzenbacher, R;Godzik, A;Jaroszewski, L
许多晶体学蛋白质结构正在使用分子替代（MR）来确定，这是一种基于模型的分相方法，随着PDB的稳定增长，这种方法变得越来越重要。虽然有几个高度自动化的MR软件包，但准备MR最佳搜索模型的方法相对来说还没有被探索过。序列比较方法的最新进展允许检测更多的远亲同源物和更准确的序列比对。研究了基于这些改进方法的比对的简单同源模型（没有对未对齐区域建模）是否能够增加MR. 27晶体结构的潜力，并使用高度并行的MR管道确定了MR. 27晶体结构，该管道促进了包括同源检测、模型制备、MR搜索、自动精化和重建在内的所有步骤。用标准序列-序列比对（BLAST）和更精确的序列-序列和序列-序列比对方法（PSI-BLAST， FFAS）制备的几种搜索模型在MR试验中进行了比较。分析表明，当未知结构与搜索模型的序列同一性小于35%时，基于更精确比对的模型成功率更高。结果表明，在精确对准的基础上使用不同类型的简单模型，可以显著提高MR的成功率。
Many crystallographic protein structures are being determined using molecular replacement (MR), a model-based phasing method that has become increasingly important with the steady growth of the PDB. While there are several highly automated software packages for MR, the methods for preparing optimal search models for MR are relatively unexplored. Recent advances in sequence-comparison methods allow the detection of more distantly related homologs and more accurate alignment of their sequences. It was investigated whether simple homology models ( without modeling of unaligned regions) based on alignments from these improved methods are able to increase the potential of MR. 27 crystal structures were determined using a highly parallelized MR pipeline that facilitates all steps including homology detection, model preparation, MR searches, automated refinement and rebuilding. Several types of search models prepared with standard sequence - sequence alignment ( BLAST) and more accurate profile - sequence and profile - profile methods (PSI-BLAST, FFAS) were compared in MR trials. The analysis shows that models based on more accurate alignments have a higher success rate in cases where the unknown structure and the search model share less than 35% sequence identity. It is concluded that by using different types of simple models based on accurate alignments, the success rate of MR can be significantly increased.