PDB MANAGEMENT BY THE RESEARCH COLLABORATORY FOR STRUCTURAL BIOINFORMATICS

结构生物信息学研究合作实验室的 PDB 管理

基本信息

批准号：
10686902
负责人：
STEPHEN K BURLEY
金额：
$ 349.2万
依托单位：
RUTGERS, THE STATE UNIV OF N.J.
依托单位国家：
美国
项目类别：
财政年份：
2019
资助国家：
美国
起止时间：
2019-08-01 至 2024-07-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10686902
关键词：
3-Dimensional Address Affect Animals Archives Area Automobile Driving Award Biochemical Pathway Biocompatible Materials Bioinformatics Biological Biological Process Biological Products Biology Biomedical Research Biotechnology Cell physiology Cells Climacteric Cloud Computing Communicable Diseases Communities Cryo-electron tomography Crystallography Data Deposition Development Disease Education Education and Outreach Electron Microscopy Facility Ensure FAIR principles Failure Food Fostering Growth Health Human Resources Hybrids Investments Knowledge Legal patent Life Life Cycle Stages Macromolecular Complexes Measurement Medical Device Methods Mission Molecular Biology Molecular Evolution Molecular Machines Neurosciences Pharmacologic Substance Plants Production Public Domains Publications Reproducibility Research Research Personnel Science Services Shapes Software Engineering Source Structure Students Synchrotrons Techniques Therapeutic Time United States National Institutes of Health Universities Validation Work X-Ray Crystallography applied biomedical research collaboratory cost data exploration data repository data resource drug development drug discovery human disease innovation macromolecule member new therapeutic target novel therapeutics online delivery particle protein data bank recruit research and development structural biology three dimensional structure tool x-ray free-electron laser

项目摘要

PROJECT SUMMARY The mission of the Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) is to sustain a unique Findable-Accessible-Interoperable-Reusable living data resource of three-dimensional (3D) biomolecular structure information. PDB structures are the molecules of life. Knowledge of 3D structures (shapes) of biological macromolecules, how they evolved with time, and their functions are essential for understanding critical areas of science, including fundamental biology; health and disease of humans, animals, and plants; food and energy production; and other topics of concern to global prosperity and environmental sustainability. Structure data are equally important for biopharmaceutical and biotechnology companies, driving discovery of new therapeutics, biomaterials, and medical devices. RCSB PDB services span the entire PDB data lifecycle, encompassing Deposition/Biocuration, Archive Management/Access, Data Exploration, and Outreach/Education. RCSB PDB Archive Management/Access services safeguard the single global archive of >144,000 3D structures of biological macromolecules, with an estimated replacement cost of nearly $14 billion. RCSB PDB Deposition/Biocuration and Data Exploration services support >30,000 Data Depositors and >1 million Data Consumers worldwide. More than 620,000 researchers, educators, students, and members of the public use our award winning Outreach/Education Services. During 2019-2023, the RCSB PDB has three Specific Aims. Successful completion of these Specific Aims will entail further investments in cloud computing/storage, considerable software engineering, and modest recruitment of additional personnel to address three overarching challenges that confront the organization. Specific Aim 1: Scale RCSB PDB operational capabilities to meet projected growth in (i) new structures; (ii) average structure size and complexity; (iii) annual data download volume; and (iv) Users and User communities, and diversity thereof. Specific Aim 2: Scale RCSB PDB operational capabilities to meet projected growth in structure data and complexity coming from studies of molecular machines using two rapidly evolving experimental methods (serial femtosecond X-ray crystallography or SFX and 3DEM) that have already eclipsed some of our service capabilities. Specific Aim 3: Implement deposition-validation-biocuration, archiving, and online delivery/tooling for structure data from emerging structure determination methods that combine 3DEM and/or macromolecular crystallography with multiple measurement techniques not currently supported in the PDB. These Integrative/Hybrid Methods structures are in the vanguard of cell/organismal biology research. Continued access to PDB data and RCSB PDB Services will drive publication of innovative research across the biomedical sciences, drug discovery and development, patent applications, and innovations leading to discovery and development of life-changing biopharmaceutical products and formation of new US companies.

项目概要结构生物信息学蛋白质数据库研究合作实验室 (RCSB PDB) 的使命是维持独特的可查找、可访问、可互操作、可重用的三维 (3D) 生活数据资源生物分子结构信息。 PDB结构是生命的分子。 3D 结构知识生物大分子（形状）、它们如何随时间演变以及它们的功能对于了解科学的关键领域，包括基础生物学；人类、动物的健康和疾病，和植物；粮食和能源生产；以及其他关注全球繁荣和环境的话题可持续性。结构数据对于生物制药和生物技术公司同样重要，推动新疗法、生物材料和医疗设备的发现。 RCSB PDB服务跨越整个PDB数据生命周期，包括沉积/生物管理、档案管理/访问、数据探索和外展/教育。 RCSB PDB 档案管理/访问服务可保护单个全球档案 > 144,000 个生物大分子 3D 结构，估计重置成本近 140 亿美元。 RCSB PDB 沉积/生物管理和数据探索服务支持 >30,000 个数据存储者和 >1 全球数百万数据消费者。超过 620,000 名研究人员、教育工作者、学生和成员公众使用我们屡获殊荣的外展/教育服务。 2019-2023 年期间，RCSB PDB 有三个具体目标。成功完成这些具体目标将需要对云计算/存储、大量软件工程以及适度的投资进行进一步投资征聘更多人员来应对本组织面临的三大挑战。具体目标 1：扩展 RCSB PDB 运营能力，以满足 (i) 新结构的预计增长； (ii) 平均结构尺寸和复杂性； (iii) 年度数据下载量； (iv) 用户和用户社区及其多样性。具体目标 2：扩展 RCSB PDB 运营能力以满足预期使用两种快速发展的分子机器研究导致结构数据和复杂性的增长已经黯然失色的实验方法（串行飞秒 X 射线晶体学或 SFX 和 3DEM）我们的一些服务能力。具体目标 3：实施沉积-验证-生物管理、归档和结合 3DEM 的新兴结构确定方法的结构数据在线交付/工具和/或具有多种测量技术的大分子晶体学，目前尚不支持 PDB。这些综合/混合方法结构处于细胞/有机体生物学研究的前沿。持续访问 PDB 数据和 RCSB PDB 服务将推动整个领域创新研究的发表生物医学、药物发现和开发、专利申请以及导致发现的创新开发改变生活的生物制药产品以及组建新的美国公司。