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首页> 美国卫生研究院文献>Nucleic Acids Research >PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features
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PASS2 database for the structure-based sequence alignment of distantly related SCOP domain superfamilies: update to version 5 and added features

机译：PASS2数据库用于对远距离相关的SCOP域超家族进行基于结构的序列比对：更新至版本5和新增的功能

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摘要

Structure-based sequence alignment is an essential step in assessing and analysing the relationship of distantly related proteins. PASS2 is a database that records such alignments for protein domain superfamilies and has been constantly updated periodically. This update of the PASS2 version, named as PASS2.5, directly corresponds to the SCOPe 2.04 release. All SCOPe structural domains that share less than 40% sequence identity, as defined by the ASTRAL compendium of protein structures, are included. The current version includes 1977 superfamilies and has been assembled utilizing the structure-based sequence alignment protocol. Such an alignment is obtained initially through MATT, followed by a refinement through the COMPARER program. The JOY program has been used for structural annotations of such alignments. In this update, we have automated the protocol and focused on inclusion of new features such as mapping of GO terms, absolutely conserved residues among the domains in a superfamily and inclusion of PDBs, that are absent in SCOPe 2.04, using the HMM profiles from the alignments of the superfamily members and are provided as a separate list. We have also implemented a more user-friendly manner of data presentation and options for downloading more features. PASS2.5 version is available at .
机译：基于结构的序列比对是评估和分析远距离相关蛋白质之间关系的重要步骤。 PASS2是一个数据库，它记录蛋白质结构域超家族的此类比对，并定期进行定期更新。 PASS2版本的此更新名为PASS2.5，直接对应于SCOPe 2.04版本。如蛋白质结构的ASTRAL纲要所定义，所有共享少于40％序列同一性的SCOPe结构域都包括在内。当前版本包括1977个超家族，并已使用基于结构的序列比对协议进行组装。首先通过MATT获得这种对齐方式，然后通过COMPARER程序进行优化。 JOY程序已用于此类路线的结构注释。在此更新中，我们使该协议自动化，并专注于包括新功能，例如GO术语的映射，超家族中域之间绝对保守的残基以及SCOPe 2.04中不存在的PDB，使用来自超家族成员的排列，并作为单独的列表提供。我们还实现了一种更加用户友好的数据表示方式，并提供了用于下载更多功能的选项。可通过访问PASS2.5版本。

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