14 NSFBIO:Towards detailed and consistent function prediction from protein family databases

14 NSFBIO：从蛋白质家族数据库进行详细且一致的功能预测

• 批准号: BB/N00521X/1
• 负责人: Robert Finn
• 金额: $ 58万
• 依托单位: European Bioinformatics Institute
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2015
• 资助国家: 英国
• 起止时间: 2015 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FN00521X%2F1
• 关键词: 14; NSFBIO; Towards; detailed; consistent

Significance. Thanks to continuing developments in DNA sequencing technology, we now know the exact genetic makeup ("genome") of thousands of different organisms, encoding millions of different proteins. But simply knowing the chemical specification (the "sequence") of these proteins is only a first step-the ultimate goal is to discover how genes and proteins function to support the diversity of life, and also how some of them can be used for commercial and biotechnology applications. This research project will expand the capability of scientists and their students, to advance their analyses from sequences to functions, by bringing together multiple different state-of-the-art approaches. Each of these approaches uses both computational (necessary to address a problem of this magnitude) and broad biological expertise. Approach. The general approach in this project is to classify proteins into families of related proteins, and, wherever possible, describe how each family relates to function. The ultimate goal is to assign the same specific function to all of the proteins in a family or to subsets of the family if more than one function is represented within the family. These relations may be very complex, and scientific accuracy will require application of multiple, diverse methods. In order to accomplish this aim, the project will expand InterPro, a widely used resource that already contains (though with limited data integration mechanisms) eleven different databases, three of which are involved in this project: PANTHER, Pfam and TIGRFAM. A fourth classification resource, the Structure-Function Linkage Database (SFLD), will also be incorporated into InterPro. These four databases use complementary methodologies to represent and describe protein relationships, which will be integrated to address the problem of protein function classification with unprecedented accuracy, precision and ease-of-use. As proteins do not generally work in isolation, additional structured annotations relating to pathways and complexes will be added to sets of families, to defined functional characteristics present in a genome. The products of this work will be used to enhance sequence analysis tools used by the scientific community, as well as to provide enhanced educational materials, and will be broadly accessible over the web at http://ebi.ac.uk/interpro.

意义由于DNA测序技术的不断发展，我们现在知道了数千种不同生物体的确切基因组成（“基因组”），编码数百万种不同的蛋白质。但简单地了解这些蛋白质的化学规格（“序列”）只是第一步-最终目标是发现基因和蛋白质如何发挥作用来支持生命的多样性，以及其中一些如何用于商业和生物技术应用。该研究项目将扩大科学家及其学生的能力，通过汇集多种不同的最先进的方法，将他们的分析从序列推进到功能。这些方法中的每一种都使用了计算（解决这种规模的问题所必需的）和广泛的生物学专业知识。Approach.本项目的一般方法是将蛋白质分类为相关蛋白质家族，并尽可能描述每个家族与功能的关系。最终目标是将相同的特定功能分配给家族中的所有蛋白质或家族的子集，如果家族中有一个以上的功能。这些关系可能非常复杂，科学的准确性将需要应用多种多样的方法。为了实现这一目标，该项目将扩大InterPro，这是一个广泛使用的资源，已经包含（尽管数据集成机制有限）11个不同的数据库，其中三个涉及该项目：PANTHER，Pfam和TIGRFAM。第四个分类资源，结构-功能链接数据库（SFLD），也将被纳入InterPro。这四个数据库使用互补的方法来表示和描述蛋白质的关系，这将被整合，以解决蛋白质功能分类的问题，具有前所未有的准确性，精度和易用性。由于蛋白质通常不会孤立地起作用，因此与途径和复合物相关的额外结构化注释将被添加到家族集合中，以定义基因组中存在的功能特征。这项工作的产品将用于增强科学界使用的序列分析工具，以及提供增强的教育材料，并将在http://ebi.ac.uk/interpro网站上广泛提供。

项目成果

Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes.

• DOI: 10.1093/nar/gky1013
• 发表时间: 2019-01-08
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Richardson LJ;Rawlings ND;Salazar GA;Almeida A;Haft DR;Ducq G;Sutton GG;Finn RD
• 通讯作者: Finn RD

InterPro in 2017-beyond protein family and domain annotations.

• DOI: 10.1093/nar/gkw1107
• 发表时间: 2017-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Finn RD;Attwood TK;Babbitt PC;Bateman A;Bork P;Bridge AJ;Chang HY;Dosztányi Z;El-Gebali S;Fraser M;Gough J;Haft D;Holliday GL;Huang H;Huang X;Letunic I;Lopez R;Lu S;Marchler-Bauer A;Mi H;Mistry J;Natale DA;Necci M;Nuka G;Orengo CA;Park Y;Pesseat S;Piovesan D;Potter SC;Rawlings ND;Redaschi N;Richardson L;Rivoire C;Sangrador-Vegas A;Sigrist C;Sillitoe I;Smithers B;Squizzato S;Sutton G;Thanki N;Thomas PD;Tosatto SC;Wu CH;Xenarios I;Yeh LS;Young SY;Mitchell AL
• 通讯作者: Mitchell AL

TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations

TreeGrafter：使用基因本体术语和其他注释对蛋白质进行基于系统发育树的注释

• DOI: 10.48550/arxiv.1802.07304
• 发表时间: 2018
• 作者: Tang H

TreeGrafter: phylogenetic tree-based annotation of proteins with Gene Ontology terms and other annotations.

• DOI: 10.1093/bioinformatics/bty625
• 发表时间: 2019-02-01
• 期刊: Bioinformatics (Oxford, England)
• 作者: Tang H;Finn RD;Thomas PD
• 通讯作者: Thomas PD

The MEROPS database of proteolytic enzymes, their substrates and inhibitors in 2017 and a comparison with peptidases in the PANTHER database.

• DOI: 10.1093/nar/gkx1134
• 发表时间: 2018-01-04
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Rawlings ND;Barrett AJ;Thomas PD;Huang X;Bateman A;Finn RD
• 通讯作者: Finn RD