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

• 批准号: 10224778
• 负责人: STEPHEN K BURLEY
• 金额: $ 342.27万
• 依托单位: RUTGERS, THE STATE UNIV OF N.J.
• 依托单位国家: 美国
• 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/10224778
• 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 Energy; Fostering; Growth; Health; Human Resources; Hybrids; Investments; Knowledge; Legal patent; Life; 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 complexity; 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

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.

项目摘要 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 维持一个独特可发现、可共享、可互操作、可重用的三维（3D）活体数据资源 生物分子结构信息。PDB结构是生命的分子。了解3D结构 生物大分子的形状，它们如何随着时间的推移而进化，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， 粮食和能源生产;以及其他与全球繁荣和环境 持续发展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、生物材料和医疗器械的发现。RCSB PDB服务跨越整个PDB数据 生命周期，包括沉积/生物固化、档案管理/访问、数据探索和 外联/教育。RCSB PDB存档管理/访问服务保护了 > 144，000个生物大分子的3D结构，估计更换成本近140亿美元。 RCSB PDB沉积/生物固化和数据探索服务支持> 30，000个数据存储器和>1 全球数百万数据消费者。超过62万名研究人员，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。 在2019-2023年期间，RCSB PDB有三个具体目标。这些具体目标的成功实现将 需要进一步投资云计算/存储，大量的软件工程，以及适度的 征聘更多人员，以应对本组织面临的三大挑战。 具体目标1：扩大RCSB PDB的业务能力，以满足（一）新结构的预期增长; (ii)平均结构规模和复杂性;（iii）每年数据下载量;以及（iv）用户和用户 社区及其多样性。具体目标2：扩大RCSB PDB的运营能力，以满足预计的 结构数据和复杂性的增长来自于使用两种快速进化的分子机器的研究 实验方法（连续飞秒X射线晶体学或SFX和3DEM）已经黯然失色 我们的一些服务能力。具体目标3：实现沉积-验证-生物定位、存档和 在线交付/加工来自新兴结构确定方法的结构数据，这些方法结合了联合收割机3DEM 和/或大分子晶体学，其中多个测量技术目前在 PDB。这些综合/混合方法结构是细胞/有机体生物学研究的先锋。 持续访问PDB数据和RCSB PDB服务将推动整个地区创新研究的出版。 生物医学科学、药物发现和开发、专利申请和导致发现的创新 和改变生活的生物制药产品的开发和新的美国公司的形成。