FunTree: advances in a resource for exploring and contextualising protein function evolution
FunTree: advances in a resource for exploring and contextualising protein function evolution
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FunTree：探索和背景化蛋白质功能进化的资源进展
DOI：
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发表时间：
2015
期刊：
影响因子：
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通讯作者：
Nicholas Furnham
中科院分区：
文献类型：
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作者：
I. Sillitoe;Nicholas Furnham
FunTree是一个汇集蛋白质序列，结构和功能信息的资源，包括整体化学反应和机械数据，用于结构定义的结构域超家族。最初的FunTree与CATH数据库一起开发，仅包含276个专注于酶的超家族。在这里，我们提出了一个更新的FunTree，已扩展到包括2340个超家族，包括酶和蛋白质与非酶功能注释的基因本体论（GO）术语。这允许调查新功能如何在结构定义的超家族中进化，并提供了一种分析许多超家族趋势的方法。这不仅在蛋白质的序列和结构的背景下进行，而且在它们的功能的关系中进行。功能相似性的新措施已被整合，包括酶的整体反应的基础上的整体键的变化，反应中心（参与反应的局部环境原子）和参与反应的代谢产物的子结构相似性和非酶的语义相似性的基础上的GO比较。为了识别和突出功能的变化，通过进化，祖先的性格估计和提出。所有这些都可以通过一个新的重新设计的Web界面访问，该界面可以在http://www.funtree.info上找到。
FunTree is a resource that brings together protein sequence, structure and functional information, including overall chemical reaction and mechanistic data, for structurally defined domain superfamilies. Developed in tandem with the CATH database, the original FunTree contained just 276 superfamilies focused on enzymes. Here, we present an update of FunTree that has expanded to include 2340 superfamilies including both enzymes and proteins with non-enzymatic functions annotated by Gene Ontology (GO) terms. This allows the investigation of how novel functions have evolved within a structurally defined superfamily and provides a means to analyse trends across many superfamilies. This is done not only within the context of a protein's sequence and structure but also the relationships of their functions. New measures of functional similarity have been integrated, including for enzymes comparisons of overall reactions based on overall bond changes, reaction centres (the local environment atoms involved in the reaction) and the sub-structure similarities of the metabolites involved in the reaction and for non-enzymes semantic similarities based on the GO. To identify and highlight changes in function through evolution, ancestral character estimations are made and presented. All this is accessible through a new re-designed web interface that can be found at http://www.funtree.info.