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

点击翻译按钮获取中文摘要

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