Protein structure alignment using environmental profiles
Protein structure alignment using environmental profiles
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DOI：
10.1093/protein/13.8.535
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发表时间：
2000-08-01
期刊：
影响因子：
--
通讯作者：
Lee, B
中科院分区：
文献类型：
--
作者：
Jung, J;Lee, B
描述了一种新的蛋白质结构比对程序。初始比对是通过比较两种蛋白质的一级、二级和三级结构特征（概况）的一维列表来进行的，而不明确考虑结构的三维几何形状。然后在第二步中迭代地细化对齐，其中通过基于当前对齐的结构的三维叠加来找到新的对齐。这个新程序足够快，可以常规地进行全面的结构比较。该过程有时会发现一种表明进化关系的对齐方式，而如果仅考虑几何形状，通常无法获得这种对齐方式。所有成对比较均在代表所有已知蛋白质结构的 3539 个蛋白质结构域之间进行。所得的 3539 个 z 分数用于对蛋白质进行聚类，随着 z 截止值的提高，主要簇的数量不断增加，但多成员簇的数量在 z 截止值 5.0 和 5.5 时显示出最大值。当使用 z 截止值为 5.0 时，主簇总数为 2043 个，其中只有 336 个簇具有超过 1 个成员。
A new protein structure alignment procedure is described. An initial alignment is made by comparing a one-dimensional list of primary, secondary and tertiary structural features (profiles) of two proteins, without explicitly considering the three-dimensional geometry of the structures. The alignment is then iteratively refined in the second step, in which new alignments are found by three-dimensional superposition of the structures based on the current alignment. This new procedure is fast enough to do all-against-all structural comparisons routinely. The procedure sometimes finds an alignment that suggests an evolutionary relationship and which is not normally obtained if only geometry is considered. All pair-wise comparisons were made among 3539 protein structural domains that represent all known protein structures. The resulting 3539 z-scores were used to cluster the proteins, The number of main clusters increased continuously as the z-cutoff was raised, but the number of multiple-member clusters showed a maximum at z-cutoff values of 5.0 and 5.5. When a z-cutoff value of 5.0 was used, the total number of main clusters was 2043, of which only 336 clusters had more than one member.