Support for the SUPERFAMILY protein domain resource.

支持 SUPERFAMILY 蛋白质域资源。

• 批准号: BB/G022771/1
• 负责人: Julian Gough
• 金额: $ 87.21万
• 依托单位: University of Bristol
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2010
• 资助国家: 英国
• 起止时间: 2010 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FG022771%2F1
• 关键词: Support; SUPERFAMILY; protein; domain; resource.

The SUPERFAMILY resource detects and classifies protein domains of known structure in genome sequences. Small proteins are a single unit but larger proteins can be made up of multiple subunits we call domains. Domains are modular evolutionary blocks which are assembled into whole proteins via duplication and recombination. X-ray crystallography and NMR experiments provide the 3D atomic resolution of proteins allowing the domains to be grouped into related families which often share a common or related function. The SUPERFAMILY database contains a library of profiles of these domain families in the form of hidden Markov models. These models are a computational tool which can detect the presence of domains in the sequences of proteins. Some years ago the first complete genome was experimentally characterised, giving us a list of all the sequences of the proteins which make up that organism. Subsequently the human genome was sequenced and now we have the complete sequences for the proteins of approaching 1,000 organisms. The SUPERFAMILY model library is run against all the genomes to identify the domains in the proteins. Our knowledge of domain families is not complete, so the assignments from the hidden Markov models cover only about half of the protein sequences, but this is still extremely valuable information. The data produced by the SUPERFAMILY analysis can be used for example by biologists working on specific proteins in the laboratory, larger projects working on a whole genome, or to improve our understanding of molecular evolution across all genomes and all kingdoms of life. The SUPERFAMILY website enables users to enter sequences to search against the model library. The results of the domain assignments to all the genomes are stored in a database and can also be viewed on the website. There are many tools and ways of browsing the data which allow the comparison of different organisms, proteins and domains to allow researchers to answer biological questions. The data,software and model library are available for people to download wholesale to carry out their own analysis. The information contained in SUPERFAMILY feeds into several other websites and resources, e.g. the ENSEMBL human genome website, which bring together different specialist sources of data to display alongside each other.

SUPERFAMILY资源检测和分类基因组序列中已知结构的蛋白质结构域。小的蛋白质是一个单一的单位，但较大的蛋白质可以由多个亚基组成，我们称之为结构域。结构域是通过复制和重组组装成整个蛋白质的模块化进化块。X射线晶体学和NMR实验提供了蛋白质的3D原子分辨率，允许将结构域分组为通常具有共同或相关功能的相关家族。SUPERFAMILY数据库包含了一个以隐马尔可夫模型形式的这些域族的配置文件库。这些模型是一种计算工具，可以检测蛋白质序列中结构域的存在。几年前，第一个完整的基因组通过实验得到了表征，给了我们一个组成该生物体的所有蛋白质序列的列表。随后，人类基因组被测序，现在我们有近1,000种生物的蛋白质的完整序列。SUPERFAMILY模型库针对所有基因组运行以识别蛋白质中的结构域。我们对结构域家族的知识并不完整，因此隐马尔可夫模型的赋值只覆盖了大约一半的蛋白质序列，但这仍然是非常有价值的信息。SUPERFAMILY分析产生的数据可用于例如在实验室中研究特定蛋白质的生物学家，研究整个基因组的大型项目，或提高我们对所有基因组和所有生命王国的分子进化的理解。SUPERFAMILY网站允许用户输入序列以搜索模型库。所有基因组的域分配结果存储在数据库中，也可以在网站上查看。有许多浏览数据的工具和方法，可以比较不同的生物体，蛋白质和结构域，让研究人员回答生物学问题。数据、软件和模型库可供人们批量下载，以进行自己的分析。SUPERFAMILY中包含的信息可以输入到其他几个网站和资源中，例如ENSEMBL人类基因组网站，该网站汇集了不同的专业数据来源，相互显示。

项目成果

Performance of in silico tools for the evaluation of p16INK4a (CDKN2A) variants in CAGI.

• DOI: 10.1002/humu.23235
• 发表时间: 2017-09
• 期刊: Human mutation
• 影响因子: 3.9
• 作者: Carraro M;Minervini G;Giollo M;Bromberg Y;Capriotti E;Casadio R;Dunbrack R;Elefanti L;Fariselli P;Ferrari C;Gough J;Katsonis P;Leonardi E;Lichtarge O;Menin C;Martelli PL;Niroula A;Pal LR;Repo S;Scaini MC;Vihinen M;Wei Q;Xu Q;Yang Y;Yin Y;Zaucha J;Zhao H;Zhou Y;Brenner SE;Moult J;Tosatto SCE
• 通讯作者: Tosatto SCE

SUPERFAMILY 1.75 including a domain-centric gene ontology method.

• DOI: 10.1093/nar/gkq1130
• 发表时间: 2011-01
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: de Lima Morais DA;Fang H;Rackham OJ;Wilson D;Pethica R;Chothia C;Gough J
• 通讯作者: Gough J

The genome of Aiptasia, a sea anemone model for coral symbiosis

Aiptasia 的基因组，一种珊瑚共生的海葵模型

• DOI: 10.1073/pnas.1513318112
• 发表时间: 2015-09-22
• 期刊: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• 影响因子: 11.1
• 作者: Baumgarten, Sebastian;Simakov, Oleg;Voolstra, Christian R.
• 通讯作者: Voolstra, Christian R.

The 'dnet' approach promotes emerging research on cancer patient survival.

• DOI: 10.1186/s13073-014-0064-8
• 发表时间: 2014
• 期刊: Genome medicine
• 影响因子: 12.3
• 作者: Fang H;Gough J
• 通讯作者: Gough J

Matching phenotypes to whole genomes: Lessons learned from four iterations of the personal genome project community challenges.

• DOI: 10.1002/humu.23265
• 发表时间: 2017-09
• 期刊: Human mutation
• 影响因子: 3.9
• 作者: Cai B;Li B;Kiga N;Thusberg J;Bergquist T;Chen YC;Niknafs N;Carter H;Tokheim C;Beleva-Guthrie V;Douville C;Bhattacharya R;Yeo HTG;Fan J;Sengupta S;Kim D;Cline M;Turner T;Diekhans M;Zaucha J;Pal LR;Cao C;Yu CH;Yin Y;Carraro M;Giollo M;Ferrari C;Leonardi E;Tosatto SCE;Bobe J;Ball M;Hoskins RA;Repo S;Church G;Brenner SE;Moult J;Gough J;Stanke M;Karchin R;Mooney SD
• 通讯作者: Mooney SD