Selection of representative protein data sets
Selection of representative protein data sets
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DOI：
10.1002/pro.5560010313
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发表时间：
1992-03
期刊：
影响因子：
8
通讯作者：
U. Hobohm;M. Scharf;R. Schneider;C. Sander
中科院分区：
文献类型：
--
作者：
U. Hobohm;M. Scharf;R. Schneider;C. Sander
蛋白质数据库目前包含约 600 个通过 X 射线晶体学或 NMR 确定的三维蛋白质坐标数据集。数据库中存在相当大的冗余，因为许多蛋白质对的序列相同或非常相似。然而，蛋白质序列结构关系的统计分析需要非冗余数据。我们开发了两种算法来从数据库中提取具有最大覆盖度和最小冗余度的代表性蛋白质链集。第一个算法侧重于优化所选蛋白质的特定属性，并通过从有序列表中连续选择蛋白质并排除每个所选蛋白质的所有邻居来工作。另一种算法旨在最大化所选集合的大小，并通过连续稀疏相似蛋白质的簇来工作。这两种算法通常适用于可以定义相似性标准并与图论问题相关的其他数据库。从当前版本的蛋白质数据库中提取的最大非冗余集有 155 条蛋白质链。在这个集合中，没有两个蛋白质的序列相似性高于一定的截止值（比对的子序列超过 80 个残基，有 30% 相同的残基），但所有结构独特的蛋白质家族都被代表。可通过文件服务器“netserv@embl‐heidelberg.de”通过电子邮件获取定期更新的代表性数据集列表。该选择可能有助于蛋白质折叠的统计方法以及已知的三维蛋白质结构谱的分析和记录。
The Protein Data Bank currently contains about 600 data sets of three‐dimensional protein coordinates determined by X‐ray crystallography or NMR. There is considerable redundancy in the data base, as many protein pairs are identical or very similar in sequence. However, statistical analyses of protein sequence‐structure relations require nonredundant data. We have developed two algorithms to extract from the data base representative sets of protein chains with maximum coverage and minimum redundancy. The first algorithm focuses on optimizing a particular property of the selected proteins and works by successive selection of proteins from an ordered list and exclusion of all neighbors of each selected protein. The other algorithm aims at maximizing the size of the selected set and works by successive thinning out of clusters of similar proteins. Both algorithms are generally applicable to other data bases in which criteria of similarity can be defined and relate to problems in graph theory. The largest nonredundant set extracted from the current release of the Protein Data Bank has 155 protein chains. In this set, no two proteins have sequence similarity higher than a certain cutoff (30% identical residues for aligned subsequences longer than 80 residues), yet all structurally unique protein families are represented. Periodically updated lists of representative data sets are available by electronic mail from the file server “netserv@embl‐heidelberg.de.” The selection may be useful in statistical approaches to protein folding as well as in the analysis and documentation of the known spectrum of three‐dimensional protein structures.