Gene3D: merging structure and function for a Thousand genomes.
Gene3D: merging structure and function for a Thousand genomes.
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DOI：
10.1093/nar/gkp987
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发表时间：
2010-01
影响因子：
14.9
通讯作者：
Orengo C
中科院分区：
文献类型：
--
作者：
Lees J;Yeats C;Redfern O;Clegg A;Orengo C
在过去的两年中，Gene3D资源得到了显着改善，现在更准确，并且通过Gene3D网站（http://gene3d.biochem.ucl.ac.ac.uk/）进行了更丰富的交互式显示。 Gene3d为超过1100个基因组和近1万蛋白质提供了准确的结构结构域家族分配。由手动策划的CATH结构域层次结构构建的隐藏的Markov模型库用于搜索Uniprot，RefSeq和Ensembl蛋白序列。使用最近开发的内部算法，DomainFinder 3（可在：ftp：//ftp.biochem.ucl.ucl.ac.uk/pub/pub/gene3d_data/domainfinder3/）中，将结果匹配改进为简单的多域架构。域分配与多个外部蛋白质功能描述（例如基因本体论和KEGG），结构注释（例如盘绕线圈，无序区域和序列多态性）以及家庭资源（例如PFAM和Eggnog）以及在Gene3D网站上显示。该网站允许用户查看单蛋白和基因以及大型蛋白质的描述，例如超家族或基因组。然后可以选择子集进行详细研究或相关功能，并且可以使用相互作用将探索扩展到新蛋白质。 Gene3D还提供了一组服务，包括交互式基因组覆盖图可视化器，DAS注释资源，序列搜索设施和肥皂服务。
Over the last 2 years the Gene3D resource has been significantly improved, and is now more accurate and with a much richer interactive display via the Gene3D website (http://gene3d.biochem.ucl.ac.uk/). Gene3D provides accurate structural domain family assignments for over 1100 genomes and nearly 10 000 000 proteins. A hidden Markov model library, constructed from the manually curated CATH structural domain hierarchy, is used to search UniProt, RefSeq and Ensembl protein sequences. The resulting matches are refined into simple multi-domain architectures using a recently developed in-house algorithm, DomainFinder 3 (available at: ftp://ftp.biochem.ucl.ac.uk/pub/gene3d_data/DomainFinder3/). The domain assignments are integrated with multiple external protein function descriptions (e.g. Gene Ontology and KEGG), structural annotations (e.g. coiled coils, disordered regions and sequence polymorphisms) and family resources (e.g. Pfam and eggNog) and displayed on the Gene3D website. The website allows users to view descriptions for both single proteins and genes and large protein sets, such as superfamilies or genomes. Subsets can then be selected for detailed investigation or associated functions and interactions can be used to expand explorations to new proteins. Gene3D also provides a set of services, including an interactive genome coverage graph visualizer, DAS annotation resources, sequence search facilities and SOAP services.
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影响因子：
14.9
作者：
Kanehisa M;Araki M;Goto S;Hattori M;Hirakawa M;Itoh M;Katayama T;Kawashima S;Okuda S;Tokimatsu T;Yamanishi Y
通讯作者：
Yamanishi Y
影响因子：
14.9
作者：
Wilson D;Pethica R;Zhou Y;Talbot C;Vogel C;Madera M;Chothia C;Gough J
通讯作者：
Gough J
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
影响因子：
14.9
作者：
Kersey, P;Bower, L;Apweiler, R
通讯作者：
Apweiler, R
影响因子：
14.9
作者：
Chatr-aryamontri, Andrew;Ceol, Arnaud;Palazzi, Luisa Montecchi;Nardelli, Giuliano;Schneider, Maria Victoria;Castagnoli, Luisa;Cesareni, Gianni
通讯作者：
Cesareni, Gianni