The BMRB as an evolving resource for biomolecular structure-function research

BMRB 作为生物分子结构功能研究的不断发展的资源

• 批准号: 8852654
• 负责人: JOHN LUTE MARKLEY
• 金额: $ 66.22万
• 依托单位: UNIVERSITY OF WISCONSIN-MADISON
• 依托单位国家: 美国
• 财政年份: 2014
• 资助国家: 美国
• 起止时间: 2014-05-15 至 2019-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8852654
• 关键词: Address; Adopted; Advisory Committees; Algorithmic Software; Architecture; Archives; Back; Binding; Bioinformatics; Biological; Biological Markers; Biological Process; Biomedical Research; Biomolecular Nuclear Magnetic Resonance; Carbohydrates; Chemicals; Collaborations; Communication; Communities; Computer software; Computers; Data; Data Analyses; Data Set; Databases; Deposition; Development; Disease; Emerging Technologies; Engineering; Europe; Evolution; Feeds; Funding; Goals; Health; Heterogeneity; Hybrids; Indium; Internet; Japan; Knowledge; Link; Literature; Magnetic Resonance; Magnetic Resonance Spectroscopy; Medical; Metadata; Methods; Mining; Mission; Molecular Conformation; Molecular Structure; NMR Spectroscopy; Nuclear Magnetic Resonance; Nucleic Acids; Ontology; Pathway interactions; Peer Review; Pharmaceutical Preparations; Process; Protein Chemistry; Protein Dynamics; Proteins; Relaxation; Research; Resources; Retrieval; Role; Science; Scientist; Side; Site; Software Tools; Source; Specific qualifier value; Structure; System; Techniques; Technology; Therapeutic; Training; Universities; Validation; Wisconsin; biological systems; biophysical techniques; chemical property; collaboratory; complex biological systems; computerized data processing; data exchange; data modeling; data visualization; design; flexibility; improved; innovation; innovative technologies; insight; member; next generation; novel; nucleic acid structure; protein structure; simulation; software development; spectroscopic imaging; structural biology; three dimensional structure; tool; web services

DESCRIPTION (provided by applicant): The BioMagResBank (BMRB) is the unique worldwide resource that provides free access to the wealth of information on biomolecules derived from nuclear magnetic resonance (NMR) spectroscopy. These NMR experimental data underlie the three-dimensional structures of many proteins and nucleic acids and provide important insights into their dynamics, chemical properties, and molecular interactions. BMRB maintains an open architecture and a defined and flexible data model that makes it possible to respond rapidly to changes in standards for data exchange and to the steady advances in NMR technology (greater variety of archived data and increasingly detailed associated metadata). Data archived at BMRB include primary data sets and derived results, such as chemical shifts, couplings, and cross relaxations associated with three- dimensional structures, parameters that specify local dynamics, pKa values assigned to specific sites, H- exchange rates, and evidence for conformational heterogeneity and molecular interactions. BMRB integrates these NMR data into a unified, global, macromolecular structure database of general utility to the broad scientifi community. The growing volume and diversity of data available from BMRB are catalyzing transformative scientific applications, such as the determination of protein structure and dynamics directly from chemical shifts. BMRB and its collaborators develop improved software tools for integrating the retrieval, analysis, and display of NMR data in the context of molecular structure and conformation. As a member of the World Wide Protein Data Bank (wwPDB), BMRB has close ties with the three other wwPDB partners: the Research Collaboratory for Structural Bioinformatics (RCSB), the Protein Data Bank in Europe (PDBe), and the Protein Data Bank of Japan (PDBj). The ADIT-NMR deposition system developed by BMRB in collaboration with the RCSB is responsible for acquiring over 95% of the new content brought into the archive in the past year. BMRB collaborates with developers of software tools for extracting information from NMR spectral data and for validating this information. The funds requested will enable BMRB (1) to verify, reformat, archive, and distribute new data submitted electronically, (2) to maintain a productive dialogue with users and creators of biomolecular NMR data, (3) to maintain and strengthen BMRB's role in the wwPDB, (4) to collaborate with databanks specializing in related information so that useful links are created, and (5) to interact with developers of new software and algorithms that make use of biomolecular NMR data.

描述（由申请人提供）：BioMagResBank（BMRB）是全球唯一的资源，可免费访问来自核磁共振（NMR）光谱的生物分子的丰富信息。这些NMR实验数据是许多蛋白质和核酸的三维结构的基础，并为它们的动力学，化学性质和分子相互作用提供了重要的见解。该局保持开放式结构和明确而灵活的数据模型，使其能够对数据交换标准的变化和核磁共振技术的稳步发展（存档数据种类更多，相关元数据越来越详细）作出迅速反应。在BMRB存档的数据包括原始数据集和衍生结果，例如与三维结构相关的化学位移、偶联和交叉弛豫、指定局部动力学的参数、指定给特定位点的pKa值、H-交换率以及构象异质性和分子相互作用的证据。BMRB将这些NMR数据集成到一个统一的、全球性的、对广泛的科学界具有通用性的大分子结构数据库中。BMRB提供的数据量和多样性的不断增长正在催化变革性的科学应用，例如直接从化学位移确定蛋白质结构和动力学。BMRB及其合作者开发了改进的软件工具，用于在分子结构和构象的背景下集成NMR数据的检索，分析和显示。作为世界蛋白质数据库（wwPDB）的成员，BMRB与其他三个wwPDB合作伙伴关系密切：结构生物信息学研究合作实验室（RCSB），欧洲蛋白质数据库（PDBe）和日本蛋白质数据库（PDBj）。由BMRB与RCSB合作开发的ADIT-NMR沉积系统负责获取过去一年中纳入存档的95%以上的新内容。BMRB与软件工具的开发人员合作，从NMR光谱数据中提取信息并验证这些信息。申请的资金将使BMRB能够（1）核实、重新格式化、存档和分发以电子方式提交的新数据，（2）与生物分子NMR数据的用户和创建者保持富有成效的对话，（3）保持和加强BMRB在wwPDB中的作用，（4）与专门从事相关信息的数据库合作，以便创建有用的链接，以及（5）互动。 与开发新的软件和算法，利用生物分子核磁共振数据。