The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions
The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions
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DOI：
10.1093/nar/gkn855
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发表时间：
2009-01-01
影响因子：
14.9
通讯作者：
Nishikawa, Ken
中科院分区：
文献类型：
--
作者：
Fukuchi, Satoshi;Homma, Keiichi;Nishikawa, Ken
Genomes TO Protein Structures and Functions (GTOP) 数据库（http://spock.genes.nig.ac.jp/similar togenome/gtop.html）免费提供大量有关蛋白质结构和功能的信息，这些信息是通过将各种计算工具应用于完全测序的基因组的氨基酸序列而获得的。 GTOP 以用户友好的方式包含感兴趣蛋白质的 3D 结构、蛋白质家族、功能和其他有用数据的注释，以深入了解蛋白质结构。从 1999 年最初的版本开始，GTOP 不断更新，以收获基因组计划的成果，并进行增强以提供新的信息，特别是本质上无序的区域。由于本质上无序的区域构成了蛋白质的相当一部分，并且通常发挥着至关重要的作用，尤其是在真核生物中，因此它们的分配为蛋白质的功能提供了重要的额外线索。此外，我们已将以下功能纳入 GTOP：独立于平台的结构查看器、针对 SCOP 和 Pfam 的 HMM 搜索结果、二级结构预测、真核蛋白质中外显子边界的颜色显示、基因本体术语的分配、搜索工具和主文件。
The Genomes TO Protein Structures and Functions (GTOP) database (http://spock.genes.nig.ac.jp/similar to genome/gtop.html) freely provides an extensive collection of information on protein structures and functions obtained by application of various computational tools to the amino acid sequences of entirely sequenced genomes. GTOP contains annotations of 3D structures, protein families, functions, and other useful data of a protein of interest in user-friendly ways to give a deep insight into the protein structure. From the initial 1999 version, GTOP has been continually updated to reap the fruits of genome projects and augmented to supply novel information, in particular intrinsically disordered regions. As intrinsically disordered regions constitute a considerable fraction of proteins and often play crucial roles especially in eukaryotes, their assignments give important additional clues to the functionality of proteins. Additionally, we have incorporated the following features into GTOP: a platform independent structural viewer, results of HMM searches against SCOP and Pfam, secondary structure predictions, color display of exon boundaries in eukaryotic proteins, assignments of gene ontology terms, search tools, and master files.