FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.
FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies.
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DOI：
10.1093/nar/gkr852
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发表时间：
2012-01
影响因子：
14.9
通讯作者：
Thornton JM
中科院分区：
文献类型：
--
作者：
Furnham N;Sillitoe I;Holliday GL;Cuff AL;Rahman SA;Laskowski RA;Orengo CA;Thornton JM
FunTree是一个新的资源，汇集了结构上定义的酶超家族的序列、结构、系统发育、化学和机制信息。将这些数据收集到一个单一的资源中，可以研究新的酶功能如何在结构上定义的超家族中进化，并提供一种方法来分析许多超家族的趋势。这不仅取决于酶的序列和结构，还取决于它们的反应关系。该数据库是与CATH数据库一起开发的，目前包含276个超家族，覆盖了约1800个（70%）序列分配酶反应。该资源的核心是由结构知情的多序列比对生成的系统发育树，这些比对使用了补充了结构域序列的域结构比对和基于多域架构共性的全序列比对。这些树带有功能注释，如代谢物相似性，以及来自人工管理资源的注释，如催化位点图谱和酶机制的MACiE。该资源可通过web界面免费获得：www.ebi.ac.uk/thorton-srv/databases/FunTree。
FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme's sequence and structure but also the relationships of their reactions. Developed in tandem with the CATH database, it currently comprises 276 superfamilies covering ∼1800 (70%) of sequence assigned enzyme reactions. Central to the resource are phylogenetic trees generated from structurally informed multiple sequence alignments using both domain structural alignments supplemented with domain sequences and whole sequence alignments based on commonality of multi-domain architectures. These trees are decorated with functional annotations such as metabolite similarity as well as annotations from manually curated resources such the catalytic site atlas and MACiE for enzyme mechanisms. The resource is freely available through a web interface: www.ebi.ac.uk/thorton-srv/databases/FunTree.
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影响因子：
12.3
作者：
Brown, Shoshana D;Gerlt, John A;Seffernick, Jennifer L;Babbitt, Patricia C
通讯作者：
Babbitt, Patricia C
影响因子：
14.9
作者：
UniProt Consortium
通讯作者：
UniProt Consortium
Biopython：用于计算分子生物学和生物信息学的免费 Python 工具。
DOI：
10.1093/bioinformatics/btp163
发表时间：
2009-06-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Cock PJ;Antao T;Chang JT;Chapman BA;Cox CJ;Dalke A;Friedberg I;Hamelryck T;Kauff F;Wilczynski B;de Hoon MJ
通讯作者：
de Hoon MJ
影响因子：
14.8
作者：
Furnham, Nicholas;Garavelli, John S.;Thornton, Janet M.
通讯作者：
Thornton, Janet M.
影响因子：
14.9
作者：
Holliday GL;Almonacid DE;Bartlett GJ;O'Boyle NM;Torrance JW;Murray-Rust P;Mitchell JB;Thornton JM
通讯作者：
Thornton JM