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”），编码了数百万种不同的蛋白质。但仅仅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以支持生命的多样性，以及其中一些如何用于商业用途和生物技术应用。该研究项目将扩展科学家及其学生的能力，通过汇集多种不同的最先进方法，推进从序列到功能的分析。这些方法中的每一种都使用计算（解决如此严重的问题所必需的）和广泛的生物学专业知识。方法。该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。最终目标是为一个家族中的所有蛋白质或该家族的子集分配相同的特定功能（如果该家族中存在多个功能）。这些关系可能非常复杂，科学准确性需要应用多种不同的方法。为了实现这一目标，该项目将扩展 InterPro，这是一种广泛使用的资源，已经包含（尽管数据集成机制有限）十一个不同的数据库，其中三个数据库涉及该项目：PANTHER、Pfam 和 TIGRFAM。第四个分类资源，结构-功能关联数据库 (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关系，它们将被整合起来以前所未有的准确性、精确度和易用性解决蛋白质功能分类问题。由于蛋白质通常不会单独发挥作用，因此与途径和复合物相关的附加结构化注释将被添加到家族组中，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，并提供增强的教育材料，并将通过网络广泛访问：http://ebi.ac.uk/interpro。

项目成果

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

2017年蛋白水解酶及其底物和抑制剂的MEROPS数据库以及与PANTHER数据库中肽酶的比较。

• DOI: http://dx.10.1093/nar/gkx1134
• 发表时间: 2018
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Rawlings ND

The Gene Ontology Resource: 20 years and still GOing strong.

基因本体资源：20 年且依然强劲。

• DOI: http://dx.10.1093/nar/gky1055
• 发表时间: 2019
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: The Gene Ontology Consortium

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: 10.1093/bioinformatics/bty625
• 发表时间: 2018-02-20
• 期刊: Bioinformatics
• 影响因子: 5.8
• 作者: Haiming Tang;R. Finn;P. Thomas
• 通讯作者: P. Thomas

The Gene Ontology resource: enriching a GOld mine.

基因本体资源：丰富金矿。

• DOI: http://dx.10.1093/nar/gkaa1113
• 发表时间: 2021
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Gene Ontology Consortium

InterPro in 2017-beyond protein family and domain annotations.

2017 年的 InterPro——超越蛋白质家族和结构域注释。

• DOI: http://dx.10.1093/nar/gkw1107
• 发表时间: 2017
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Finn RD