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: 8615052
• 负责人: JOHN LUTE MARKLEY
• 金额: $ 16.12万
• 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/8615052
• 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; Heterogeneity; Hybrids; Imagery; 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; design; flexibility; improved; innovation; innovative technologies; insight; member; next generation; novel; nucleic acid structure; protein structure; public health relevance; simulation; software development; structural biology; three dimensional structure; tool; web services

PROJECT SUMMARY/ABSTRACT 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 scientific 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.

项目概要/摘要 BioMagResBank (BMRB) 是全球独一无二的资源，可免费获取丰富的 来自核磁共振 (NMR) 光谱的生物分子信息。这些核磁共振 实验数据是许多蛋白质和核酸三维结构的基础，并提供 对它们的动力学、化学性质和分子相互作用的重要见解。 BMRB 维持 开放式架构和定义灵活的数据模型，使快速响应成为可能 数据交换标准的变化以及 NMR 技术的稳步进步（更多种类） 归档数据和日益详细的相关元数据）。 BMRB 存档的数据包括原始数据 集和导出的结果，例如与三相关的化学位移、耦合和交叉弛豫 维度结构、指定局部动力学的参数、分配给特定位点的 pKa 值、H- 汇率以及构象异质性和分子相互作用的证据。 BMRB 将这些 NMR 数据整合到一个统一的、全局的、通用的大分子结构数据库中 广泛的科学界。 BMRB 提供的数据量和多样性不断增长，正在推动 变革性科学应用，例如直接测定蛋白质结构和动力学 来自化学位移。 BMRB 及其合作者开发了改进的软件工具来集成 在分子结构和构象的背景下检索、分析和显示 NMR 数据。作为一个 BMRB 是世界蛋白质数据库 (wwPDB) 的成员，与其他三个 wwPDB 有着密切的联系 合作伙伴：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)。 ADIT-NMR沉积系统由 BMRB 与 RCSB 合作，负责获取 95% 以上的新内容 过去一年的档案。 BMRB 与提取信息的软件工具开发商合作 来自 NMR 光谱数据并验证该信息。所请求的资金将使 BMRB (1) 能够 验证、重新格式化、存档和分发以电子方式提交的新数据，(2) 以保持高效 与生物分子 NMR 数据的用户和创建者对话，(3) 维持和加强 BMRB 在以下方面的作用： wwPDB，(4) 与专门研究相关信息的数据库合作，以便提供有用的链接 创建，以及（5）与利用生物分子的新软件和算法的开发人员进行互动 核磁共振数据。