Profile-profile comparisons by COMPASS predict intricate homologies between protein families.
Profile-profile comparisons by COMPASS predict intricate homologies between protein families.
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DOI：
10.1110/ps.03197403
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发表时间：
2003-10
期刊：
影响因子：
--
通讯作者：
Grishin NV
中科院分区：
文献类型：
--
作者：
Sadreyev RI;Baker D;Grishin NV
最近，我们提出了一种新的蛋白质比对比较方法，COMPASS（多蛋白质比对与统计显著性评估工具）。在这里，我们提出了几个例子的PFAM蛋白质家族之间的关系，检测COMPASS，导致目前尚未解决的蛋白质结构的预测。我们讨论了相对简单的COMPASS预测，这对我们来说是新的和有趣的，这将需要大量的时间和精力来证明，即使是熟练的PSI-BLAST用户。所有提出的COMPASS命中独立地证实了其他方法，包括从头计算结构预测方法ROSETTA。由ROSETTA所做的三级结构预测被证明是有用的，以改善序列衍生的比对，因为它们是基于一个合理的折叠的多肽链，而不是从序列数据库中的信息。COMPASS预测PFAM数据库中新关系的能力表明COMPASS搜索的高灵敏度，并证实了其对于发现蛋白质家族之间以前未知的相似性的潜在价值。
Recently we proposed a novel method of alignment–alignment comparison, COMPASS (the tool for COmparison of Multiple Protein Alignments with Assessment of Statistical Significance). Here we present several examples of the relations between PFAM protein families that were detected by COMPASS and that lead to the predictions of presently unresolved protein structures. We discuss relatively straightforward COMPASS predictions that are new and interesting to us, and that would require a substantial time and effort to justify even for a skilled PSI-BLAST user. All of the presented COMPASS hits are independently confirmed by other methods, including the ab initio structure-prediction method ROSETTA. The tertiary structure predictions made by ROSETTA proved to be useful for improving sequence-derived alignments, because they are based on a reasonable folding of the polypeptide chain rather than on the information from sequence databases. The ability of COMPASS to predict new relations within the PFAM database indicates the high sensitivity of COMPASS searches and substantiates its potential value for the discovery of previously unknown similarities between protein families.
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