LPFC: an Internet library of protein family core structures.
LPFC: an Internet library of protein family core structures.
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LPFC：蛋白质家族核心结构的互联网图书馆。
DOI：
10.1002/pro.5560060127
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发表时间：
1997
期刊：
影响因子：
--
通讯作者：
Altman,RB
中科院分区：
文献类型：
--
作者：
Schmidt,R;Gerstein,M;Altman,RB
随着具有已知高分辨率结构的蛋白质分子数量的增加，有必要对这些结构进行组织，以便快速检索、比较和分析。蛋白质数据库（PDB）目前包含近5000个条目，并呈指数级增长。大多数新结构在结构上与先前报道的结构相似，可以归为科。随着每个家庭成员数量的增加，就有可能从统计上总结出每个家庭的共性和差异。我们之前报道了一种方法，用于寻找具有低空间方差的原子和具有较高空间方差的原子（即，在所有家族成员中具有相同相对位置的“核心”原子和不具有相同相对位置的“非核心”原子）。我们计算的核心结构具有生物学意义，并提供了多个结构排列的优秀定量和视觉总结。为了扩展它们的效用，我们构建了一个蛋白质家族核心库，可通过www （http://www‐smi.stanford.edu/projects/helix/LPFC/）访问。这个库是用公开可用的计算机程序自动生成的，只需要一组多个对齐作为输入。它包含每个蛋白质家族中原子的空间变化的定量分析，来自家族的平均核心结构的坐标，以及显示文件（位图和VRML格式）。在这里，我们将描述该资源，并通过比较珠蛋白家族的三个多重排列来说明其适用性。结果表明，这三种基因组合具有相似性，但与家族成员的多样性和具体的基因组合方法有关，存在着显著的差异。
As the number of protein molecules with known, high‐resolution structures increases, it becomes necessary to organize these structures for rapid retrieval, comparison, and analysis. The Protein Data Bank (PDB) currently contains nearly 5,000 entries and is growing exponentially. Most new structures are similar structurally to ones reported previously and can be grouped into families. As the number of members in each family increases, it becomes possible to summarize, statistically, the commonalities and differences within each family. We reported previously a method for finding the atoms in a family alignment that have low spatial variance and those that have higher spatial variance (i.e., the “core” atoms that have the same relative position in all family members and the “non‐core” atoms that do not). The core structures we compute have biological significance and provide an excellent quantitative and visual summary of a multiple structural alignment. In order to extend their utility, we have constructed a library of protein family cores, accessible over the World Wide Web at http://www‐smi.stanford.edu/projects/helix/LPFC/. This library is generated automatically with publicly available computer programs requiring only a set of multiple alignments as input. It contains quantitative analysis of the spatial variation of atoms within each protein family, the coordinates of the average core structures derived from the families, and display files (in bitmap and VRML formats). Here, we describe the resource and illustrate its applicability by comparing three multiple alignments of the globin family. These three alignments are found to be similar, but with some significant differences related to the diversity of family members and the specific method used for alignment.