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

基本信息

批准号：
10220987
负责人：
JEFFREY C HOCH
金额：
$ 84.78万
依托单位：
UNIVERSITY OF CONNECTICUT SCH OF MED/DNT
依托单位国家：
美国
项目类别：
财政年份：
2014
资助国家：
美国
起止时间：
2014-05-15 至 2023-03-31
项目状态：
已结题

来源：
https://reporter.nih.gov/project-details/10220987
关键词：
Advisory Committees Algorithmic Software Architecture Archives Area Benchmarking Binding Bioinformatics Biological Biological Markers Biomedical Research Biomolecular Nuclear Magnetic Resonance Charge Chemicals China Collection Communities Country Data Data Reporting Data Set Databases Deposition Development Disease Educational workshop Ensure Europe Frequencies Funding Future Harvest Hybrids Hydrogen Infrastructure Japan Journals Knowledge Ligands Link Literature Magnetic Resonance Magnetic Resonance Spectroscopy Medical Membrane Proteins Metabolic Pathway Metadata Methods Modeling Molecular Molecular Conformation Molecular Structure NMR Spectroscopy Names Natural Products Nuclear Magnetic Resonance Nucleic Acids Pharmaceutical Preparations Property Protein Dynamics Proteins RNA Relaxation Reproducibility Research Research Activity Research Personnel Research Support Resources Retrieval Role Services Software Tools Structure System Systems Biology Systems Development Technology Therapeutic Time Validation Work archive data archived data biological systems biophysical techniques chemical property collaboratory data archive data dictionary data exchange data format data modeling data repository data standards data submission data tools database structure diverse data experimental study flexibility improved insight interoperability meetings member metabolomics novel nucleic acid structure protein data bank protein structure response small molecule software development solid state nuclear magnetic resonance spectroscopic survey symposium three dimensional structure tool web site

项目摘要

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 and conformations 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 (time-domain data) acquired under defined conditions and derived results, such as chemical shifts, peak intensities, scalar couplings, dipolar couplings, relaxation rates, and cross relaxations. These parameters provide information on molecular properties such as conformation, dynamics, ligand interactions, pKa values, and hydrogen exchange rates. 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). In its role in the wwPDB BMRB sets standards for NMR data types and develops software for data deposition and validation. The funds requested will enable BMRB (1) to expand the diversity and level of coverage of biomolecular NMR data in response to community needs, (2) to verify, reformat, archive, and distribute new data submitted electronically, (3) to maintain a productive dialogue with users and creators of biomolecular NMR data, (4) to maintain and strengthen BMRB's role in the wwPDB, (5) to collaborate with databanks specializing in related information so that useful links are created, and (6) 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的三维结构和构象的基础酸并提供对其动力学、化学性质和分子相互作用的重要见解。 BMRB 维护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 存档的数据包括主要数据集（时域数据）在定义的条件下获得的和导出的结果，例如化学位移、峰值强度、标量耦合、偶极耦合、弛豫率和交叉弛豫。这些参数提供有关分子特性的信息，例如构象、动力学、配体相互作用、pKa 值和氢交换率。 BMRB 将这些 NMR 数据整合成统一的、全局的大分子结构对广大科学界具有通用性的数据库。可用数据的数量和多样性不断增长 BMRB 正在催化变革性的科学应用，例如蛋白质结构的测定和直接来自化学位移的动力学。 BMRB 及其合作者开发了改进的软件工具将 NMR 数据的检索、分析和显示集成到分子结构和构象。作为世界蛋白质数据库（wwPDB）的成员，BMRB与三者有着密切的联系其他 wwPDB 合作伙伴：结构生物信息学研究合作实验室 (RCSB)、蛋白质数据库欧洲（PDBe）和日本蛋白质数据库（PDBj）。 BMRB 在 wwPDB 中的角色制定了标准核磁共振数据类型并开发数据沉积和验证软件。所请求的资金将使 BMRB (1) 扩大生物分子 NMR 数据的多样性和覆盖水平以响应社区需要，(2) 验证、重新格式化、存档和分发以电子方式提交的新数据，(3) 维护与生物分子 NMR 数据的用户和创建者进行富有成效的对话，(4) 维护和加强 BMRB 在 wwPDB 中的作用，(5) 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 (6) 与利用生物分子 NMR 的新软件和算法的开发人员进行互动数据。