Improvement of molecular-replacement models with Sculptor.
Improvement of molecular-replacement models with Sculptor.
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DOI：
10.1107/s0907444910051218
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发表时间：
2011-04
期刊：
影响因子：
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通讯作者：
Read RJ
中科院分区：
文献类型：
--
作者：
Bunkóczi G;Read RJ
本文描述了分子置换模型改进程序Sculptor，并对所使用的算法进行了分析。
在分子置换中，可通过将序列比对中包含的信息转移到模板结构来提高模型质量。已经开发了一系列算法，这些算法利用根据在附近残基上平滑后的残基替换分数计算出的序列相似性分数来删除模型中不可靠的部分或降低其权重。这些算法与常用的成熟模型改进方法一起在Sculptor程序中得以实现。通过研究算法参数对模型质量的影响，对新算法进行了分析。与现有技术的基准测试表明，Sculptor生成的模型具有优势，尤其是在比对不可靠的情况下。使用从同一结构创建但采用不同算法参数的替代模型进行多次试验，可以显著提高成功率。
The molecular-replacement model-improvement program Sculptor is described, with an analysis of the algorithms used. In molecular replacement, the quality of models can be improved by transferring information contained in sequence alignment to the template structure. A family of algorithms has been developed that make use of the sequence-similarity score calculated from residue-substitution scores smoothed over nearby residues to delete or downweight parts of the model that are unreliable. These algorithms have been implemented in the program Sculptor, together with well established methods that are in common use for model improvement. An analysis of the new algorithms has been performed by studying the effect of algorithm parameters on the quality of models. Benchmarking against existing techniques shows that models from Sculptor compare favourably, especially if the alignment is unreliable. Carrying out multiple trials using alternative models created from the same structure but using different algorithm parameters can significantly improve the success rate.