Mddb Tools#

Configuration File: mddb_tools.json Tool Type: Local Tools Count: 2

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

Available Tools#

MDDB_get_project (Type: MDDBTool)#

Retrieve one MDDB molecular dynamics project’s simulation parameters: force field, temperature, e…

MDDB_get_project tool specification

Tool Information:

  • Name: MDDB_get_project

  • Type: MDDBTool

  • Description: Retrieve one MDDB molecular dynamics project’s simulation parameters: force field, temperature, ensemble, simulation program, chains, replica count, total simulated time, frame count, and trajectory file size. Example: accession=’MD-A001UA’ returns a 10 microsecond Amber ff99SB-ILDN simulation of the SARS-CoV-2 RNA polymerase complex. Use MDDB_search_projects to find an accession.

Parameters:

  • accession (string) (required) MDDB project accession, e.g. ‘MD-A001UA’.

Example Usage:

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

MDDB_search_projects (Type: MDDBTool)#

Search MDDB, an index of over 15,000 molecular dynamics simulation trajectories (MoDEL, BioExcel,…

MDDB_search_projects tool specification

Tool Information:

  • Name: MDDB_search_projects

  • Type: MDDBTool

  • Description: Search MDDB, an index of over 15,000 molecular dynamics simulation trajectories (MoDEL, BioExcel, DESRES-ANTON, and community depositions), by protein name or PDB id. Example: query=’kinase’ or query=’6M71’. Returns each project’s accession for use with MDDB_get_project.

Parameters:

  • query (string) (required) Protein name or PDB id, e.g. ‘kinase’, ‘6M71’.

  • limit ([‘integer’, ‘null’]) (optional) Max projects to return, 1-100. Default 25.

Example Usage:

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