Bmrb Tools

Configuration File: bmrb_tools.json Tool Type: Local Tools Count: 5

This page contains all tools defined in the bmrb_tools.json configuration file.

Available Tools

BMRB_get_entries_by_pdb_id (Type: BaseRESTTool)

Find BMRB NMR entries associated with a PDB structure. Returns BMRB entry IDs linked to a given P…

BMRB_get_entries_by_pdb_id tool specification

Tool Information:

  • Name: BMRB_get_entries_by_pdb_id

  • Type: BaseRESTTool

  • Description: Find BMRB NMR entries associated with a PDB structure. Returns BMRB entry IDs linked to a given PDB accession, with match type (BLAST or author-provided). Useful for finding NMR chemical shift data for a protein with known crystal structure.

Parameters:

  • pdb_id (string) (required) PDB entry ID (e.g., ‘1ubq’, ‘1d3z’, ‘2k39’)

Example Usage:

query = {
    "name": "BMRB_get_entries_by_pdb_id",
    "arguments": {
        "pdb_id": "example_value"
    }
}
result = tu.run(query)

BMRB_get_entries_by_uniprot (Type: BaseRESTTool)

Find BMRB NMR entries for a protein using its UniProt accession. Returns NMR data entries associa…

BMRB_get_entries_by_uniprot tool specification

Tool Information:

  • Name: BMRB_get_entries_by_uniprot

  • Type: BaseRESTTool

  • Description: Find BMRB NMR entries for a protein using its UniProt accession. Returns NMR data entries associated with the protein, allowing cross-referencing between sequence databases and NMR spectroscopy data.

Parameters:

  • uniprot_id (string) (required) UniProt accession (e.g., ‘P62988’ for ubiquitin, ‘P0DTD1’ for SARS-CoV-2 polyprotein)

Example Usage:

query = {
    "name": "BMRB_get_entries_by_uniprot",
    "arguments": {
        "uniprot_id": "example_value"
    }
}
result = tu.run(query)

BMRB_get_entry (Type: BaseRESTTool)

Get NMR data entry from the Biological Magnetic Resonance Data Bank (BMRB). Returns the full NMR-…

BMRB_get_entry tool specification

Tool Information:

  • Name: BMRB_get_entry

  • Type: BaseRESTTool

  • Description: Get NMR data entry from the Biological Magnetic Resonance Data Bank (BMRB). Returns the full NMR-STAR data for a BMRB entry including chemical shifts, coupling constants, relaxation data, structure restraints, and experimental conditions. BMRB archives NMR spectroscopy data for biological macromolecules (proteins, nucleic acids, carbohydrates) and small molecules. Entry IDs are integers (e.g., 15000 for villin headpiece, 4020 for ubiquitin).

Parameters:

  • entry_id (string) (required) BMRB entry ID (e.g., ‘15000’, ‘4020’, ‘11086’)

Example Usage:

query = {
    "name": "BMRB_get_entry",
    "arguments": {
        "entry_id": "example_value"
    }
}
result = tu.run(query)

BMRB_get_entry_citation (Type: BaseRESTTool)

Get the citation/publication information for a BMRB NMR entry in BibTeX format. Returns author li…

BMRB_get_entry_citation tool specification

Tool Information:

  • Name: BMRB_get_entry_citation

  • Type: BaseRESTTool

  • Description: Get the citation/publication information for a BMRB NMR entry in BibTeX format. Returns author list, title, journal, DOI, and year. Useful for citing NMR data sources.

Parameters:

  • entry_id (string) (required) BMRB entry ID (e.g., ‘15000’, ‘4020’)

Example Usage:

query = {
    "name": "BMRB_get_entry_citation",
    "arguments": {
        "entry_id": "example_value"
    }
}
result = tu.run(query)

BMRB_search_by_keyword (Type: BaseRESTTool)

Search BMRB (Biological Magnetic Resonance Data Bank) entries by keyword or molecule name. Return…

BMRB_search_by_keyword tool specification

Tool Information:

  • Name: BMRB_search_by_keyword

  • Type: BaseRESTTool

  • Description: Search BMRB (Biological Magnetic Resonance Data Bank) entries by keyword or molecule name. Returns matching BMRB entries with their IDs and summary information. Use the ‘database’ parameter to search either macromolecules (proteins, nucleic acids) or metabolomics small molecules.

Parameters:

  • term (string) (required) Search term (protein name, molecule name, or keyword). Examples: ‘ubiquitin’, ‘calmodulin’, ‘insulin’

  • database ([‘string’, ‘null’]) (optional) Database to search: ‘macromolecules’ (proteins/nucleic acids) or ‘metabolomics’ (small molecules). Default searches both.

Example Usage:

query = {
    "name": "BMRB_search_by_keyword",
    "arguments": {
        "term": "example_value"
    }
}
result = tu.run(query)