FunPDBe - enhancing structural and functional annotation of macromolecular structure data in the PDB by collaboration and integration

FunPDBe - 通过协作和集成增强 PDB 中大分子结构数据的结构和功能注释

• 批准号: BB/P024351/1
• 负责人: Sameer Velankar
• 金额: $ 73.97万
• 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: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=BB%2FP024351%2F1
• 关键词: FunPDBe; enhancing; structural; functional; annotation

Rapid technological and scientific advances in the field of life sciences have resulted in exponential increase in the amount and diversity of biological data. This has revolutionised life-science research and transformed it into a data driven scientific field. This transformation is also affecting our understanding of three-dimensional structures of molecules of life such as proteins. Structures of macromolecules can provide great insights into the functional mechanism of biological processes. These structural data are archived in the Protein Data Bank (PDB), one of the oldest data archives in the biomedical field. PDB was established in 1971 and now contains more than 120,000 structures of macromolecules. PDB is managed by a worldwide collaboration, wwPDB, of which Protein Data Bank in Europe (PDBe) is a founding member. The wwPDB partners accept new macromolecular structures determined by scientists across the world and standardise the way these are distributed by carrying out annotation of these newly deposited entries. This annotation is limited as far as the biological context of the macromolecule is concerned. Integrating these data with other biological information and predicted annotations can help improve our understanding of life and disease processes, help design new drug molecules, or understand the effects of genetic variation on health and disease. Combining the macromolecular structure data in the PDB with value-added annotations that provide biological context can accelerate the use of this information in improving industrial biotechnology, agricultural products and human health.The UK has world leading structural bioinformatics community that has over the years developed many data analysis tools and data resources to add biological context and value added annotations to macromolecular structure data available in the PDB. Although these resources are well used, their usage can be further improved if the issues of fragmentation of information and lack of standards for describing the annotation information are addressed. FunPDBe, is designed to address these issues by standardising the way functional annotations can be shared and by subsequently implementing a central data resource that brings together the data from the PDB with the annotations from the leading UK-based structural bioinformatics data resources.. The infrastructure developed during the project will allow integration of annotations from other data resources from around the globe, not initially involved in this project. The project will also provide uniform access to this enriched data. FunPDBe will improve sustainability, ensuring that the annotations are archived safely, are accessible for the foreseeable future, remove duplication of effort and thus protect the work and investment that has gone into developing the specialised participating data resources. Thus, FunPDBe will become a unique, open global resource, and help secure the UK's leading role in structural computational biology into the future. Our goal will be achieved through following specific activities -1. A series of workshops to establish an open forum for the UK structural bioinformatics community2. Identify and import structural and functional annotations in the FunPDBe resource using standards defined for the different data types.3. Analyse and validate annotations provided by different prediction algorithms4. Define and implement protocols and mechanisms for data collection and integration5. Provide uniform data access mechanisms using the data standards; identify and create useful representative datasets to support researcher community6. Develop training materials and deliver training workshops

生命科学领域的快速技术和科学进步导致生物数据的数量和多样性呈指数级增长。这彻底改变了生命科学研究，并将其转变为数据驱动的科学领域。这种转变也影响了我们对生命分子（如蛋白质）三维结构的理解。大分子的结构可以为了解生物过程的功能机制提供很好的见解。这些结构数据被存档在蛋白质数据库（PDB）中，这是生物医学领域最古老的数据档案之一。PDB成立于1971年，现在包含超过120,000个大分子结构。PDB由全球合作组织wwPDB管理，欧洲蛋白质数据库（PDBe）是该组织的创始成员之一。wwPDB合作伙伴接受由世界各地的科学家确定的新的大分子结构，并通过对这些新沉积的条目进行注释来标准化这些分布方式。就大分子的生物学背景而言，这种注释是有限的。将这些数据与其他生物信息和预测注释相结合，可以帮助我们提高对生命和疾病过程的理解，帮助设计新的药物分子，或者理解遗传变异对健康和疾病的影响。将PDB中的大分子结构数据与提供生物学背景的增值注释相结合，可以加速利用这些信息改善工业生物技术、农产品和人类健康。英国拥有世界领先的结构生物信息学社区，多年来开发了许多数据分析工具和数据资源，为PDB中的大分子结构数据添加生物学背景和增值注释。虽然这些资源得到了很好的利用，但如果解决了信息碎片化和缺乏描述注释信息的标准的问题，则可以进一步改进它们的使用。FunPDBe旨在通过标准化功能注释共享的方式来解决这些问题，并随后实现一个中央数据资源，该资源将来自PDB的数据与来自领先的英国结构生物信息学数据资源的注释结合在一起。项目期间开发的基础设施将允许集成来自全球各地的其他数据资源的注释，这些注释最初并未涉及该项目。该项目还将提供对这些丰富数据的统一访问。FunPDBe将提高可持续性，确保注释被安全归档，在可预见的未来可以访问，消除重复工作，从而保护开发专门参与数据资源的工作和投资。因此，FunPDBe将成为一个独特的、开放的全球资源，并有助于确保英国在未来的结构计算生物学中的领导地位。我们的目标将通过以下具体活动来实现-1。为英国结构生物信息学社区建立开放论坛的一系列研讨会2。使用为不同数据类型定义的标准，识别和导入FunPDBe资源中的结构和功能注释。分析和验证不同预测算法提供的注释4。定义和实现数据收集和集成的协议和机制5。使用数据标准提供统一的数据访问机制；识别和创建有用的代表性数据集，以支持研究人员社区6。开发培训材料并举办培训研讨会

项目成果

PDBe-KB: collaboratively defining the biological context of structural data.

• DOI: 10.1093/nar/gkab988
• 发表时间: 2022-01-07
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: PDBe-KB consortium

PDBe and PDBe-KB: Providing high-quality, up-to-date and integrated resources of macromolecular structures to support basic and applied research and education.

• DOI: 10.1002/pro.4439
• 发表时间: 2022-10
• 期刊: PROTEIN SCIENCE
• 影响因子: 8
• 作者: Varadi, Mihaly;Anyango, Stephen;Appasamy, Sri Devan;Armstrong, David;Bage, Marcus;Berrisford, John;Choudhary, Preeti;Bertoni, Damian;Deshpande, Mandar;Leines, Grisell Diaz;Ellaway, Joseph;Evans, Genevieve;Gaborova, Romana;Gupta, Deepti;Gutmanas, Aleksandras;Harrus, Deborah;Kleywegt, Gerard J.;Bueno, Weslley Morellato;Nadzirin, Nurul;Nair, Sreenath;Pravda, Lukas;Afonso, Marcelo Querino Lima;Sehnal, David;Tanweer, Ahsan;Tolchard, James;Abrams, Charlotte;Dunlop, Roisin;Velankar, Sameer
• 通讯作者: Velankar, Sameer

The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies.

• DOI: 10.1093/bib/bbaa362
• 发表时间: 2021-03-22
• 期刊: Briefings in bioinformatics
• 影响因子: 9.5
• 作者: Waman VP;Sen N;Varadi M;Daina A;Wodak SJ;Zoete V;Velankar S;Orengo C
• 通讯作者: Orengo C

PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data.

• DOI: 10.1093/bioinformatics/btab424
• 发表时间: 2021-11-05
• 期刊: Bioinformatics (Oxford, England)
• 作者: Nair S;Váradi M;Nadzirin N;Pravda L;Anyango S;Mir S;Berrisford J;Armstrong D;Gutmanas A;Velankar S
• 通讯作者: Velankar S