4SCOPmap: automated assignment of protein structures to evolutionary superfamilies.
4SCOPmap: automated assignment of protein structures to evolutionary superfamilies.
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DOI：
10.1186/1471-2105-5-197
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发表时间：
2004-12-14
影响因子：
3
通讯作者：
Grishin NV
中科院分区：
文献类型：
--
作者：
Cheek S;Qi Y;Krishna SS;Kinch LN;Grishin NV
蛋白质之间的远程同源性的推断是非常具有挑战性的，并且仍然是专家的特权。因此，使用基于进化的蛋白质结构分类的一个显著缺点是难以用自动方法将新蛋白质分配到分类方案中的独特位置。为了解决这个问题，我们已经开发了一种算法，映射蛋白质结构域现有的结构分类方案，并已将其应用到SCOP数据库。该算法采用的一般策略是联合收割机将现有的几种序列和结构比较工具的结果应用于已知结构的查询蛋白质，以找到在SCOP数据库中已分类的同源物，从而确定分类分配。该算法能够映射新解决的结构中的域到适当的SCOP超家族水平，准确率约为95%。正确映射的远程同系物的例子进行了讨论。该算法还能够识别SCOP数据库中未指定的潜在进化关系，从而有助于使其更好。映射算法的策略不限于SCOP，也可以应用于任何其他基于进化的分类方案。SCOPmap可供下载。SCOPmap程序对于将新解决的结构中的结构域分配给适当的超家族以及识别不同超家族之间的进化联系是有用的。
Inference of remote homology between proteins is very challenging and remains a prerogative of an expert. Thus a significant drawback to the use of evolutionary-based protein structure classifications is the difficulty in assigning new proteins to unique positions in the classification scheme with automatic methods. To address this issue, we have developed an algorithm to map protein domains to an existing structural classification scheme and have applied it to the SCOP database. The general strategy employed by this algorithm is to combine the results of several existing sequence and structure comparison tools applied to a query protein of known structure in order to find the homologs already classified in SCOP database and thus determine classification assignments. The algorithm is able to map domains within newly solved structures to the appropriate SCOP superfamily level with ~95% accuracy. Examples of correctly mapped remote homologs are discussed. The algorithm is also capable of identifying potential evolutionary relationships not specified in the SCOP database, thus helping to make it better. The strategy of the mapping algorithm is not limited to SCOP and can be applied to any other evolutionary-based classification scheme as well. SCOPmap is available for download. The SCOPmap program is useful for assigning domains in newly solved structures to appropriate superfamilies and for identifying evolutionary links between different superfamilies.
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DOI：
10.1073/pnas.89.22.10915
发表时间：
1992-11-15
影响因子：
11.1
作者：
HENIKOFF, S;HENIKOFF, JG
通讯作者：
HENIKOFF, JG
影响因子：
5.6
作者：
Aihara, H;Ito, Y;Shibata, T
通讯作者：
Shibata, T
影响因子：
5.6
作者：
Bauer, S;Kemter, K;Steinbacher, S
通讯作者：
Steinbacher, S
影响因子：
11.4
作者：
Cramer, P;Larson, CJ;Müller, CW
通讯作者：
Müller, CW
影响因子：
4.8
作者：
Kohno, T;Sasaki, T;Sato, K
通讯作者：
Sato, K