BMRB

BMRB archives NMR spectroscopy data for biological systems to support atomic-level structural, dynamic, and chemical analyses of proteins, peptides, nucleic acids, metabolites, natural products, and related macromolecules.

Key Features:

• Repository scope: Specialized repository for NMR spectroscopy data covering proteins, peptides, nucleic acids, metabolites, natural products, and other macromolecules.
• Deposition categories: Separates biopolymer depositions into structure determinations (including atomic coordinates and supporting PDB information) and experimental NMR datasets reporting dynamics, conformational transitions, ligand binding, and assigned chemical shifts.
• wwPDB integration: Functions as a core member of the Worldwide Protein Data Bank (wwPDB) and archives NMR-derived structural data associated with PDB entries.
• NMR-STAR format: Uses the NMR-STAR data format as the standard framework for organizing and sharing NMR data.
• Programmatic access: Provides an API and libraries in Python and R for programmatic access and manipulation of NMR-STAR formatted files.
• Analysis tools: Offers tools for data analysis, visualization, and manipulation of NMR datasets.
• Metabolite data: Includes data on metabolite concentrations in complex mixtures and chemical structure elucidation for metabolites and natural products.
• Data workflows: Supports data deposition, data retrieval, and data analysis workflows for NMR spectroscopy and for software developers.
• NMRbox integration: Provides direct data access via integration with the NMRbox platform.

Scientific Applications:

• Atomic-level structure determination: Archiving and supporting NMR-derived atomic coordinates and structural information for macromolecules.
• Dynamics and conformational studies: Reporting and analyzing molecular dynamics and conformational transitions from NMR experiments.
• Ligand binding and interactions: Documenting ligand binding and macromolecular interaction data derived from NMR spectroscopy.
• Chemical shift assignments: Storing assigned chemical shifts to support structural interpretation and resonance assignment studies.
• Metabolomics and natural product characterization: Providing concentration data and chemical structure elucidation for metabolites and natural products in complex mixtures.
• Data archiving for PDB deposition: Supporting the deposition of NMR-derived data associated with PDB entries, noting that approximately 10% of PDB structures are NMR-derived.

Methodology:

Data are organized in the NMR-STAR format and accessed programmatically via an API and Python and R libraries, with tools for analysis, visualization, manipulation, and integration with NMRbox.