Membrane Topology Tools#

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

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

Available Tools#

OPM_search_structures (Type: OPMTool)#

Search the Orientations of Proteins in Membranes database for solved structures positioned in a l…

OPM_search_structures tool specification

Tool Information:

  • Name: OPM_search_structures

  • Type: OPMTool

  • Description: Search the Orientations of Proteins in Membranes database for solved structures positioned in a lipid bilayer. Returns hydrophobic thickness in angstroms, tilt angle, and the calculated transfer free energy, plus the membrane type and protein family. Transfer energy is negative for favourable insertion. Complements EBI_predict_membrane_topology, which predicts topology from sequence: OPM reports what was measured for a solved structure. Example: query=’rhodopsin’ or query=’1uaz’.

Parameters:

  • query (string) (required) Protein name or PDB identifier, e.g. ‘rhodopsin’, ‘aquaporin’, ‘1uaz’.

  • limit ([‘integer’, ‘null’]) (optional) Maximum structures to return (default 25, max 100).

Example Usage:

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

TopDB_get_topology (Type: TopDBTool)#

Retrieve experimentally curated transmembrane topology for a protein from TopDB. Returns each seq…

TopDB_get_topology tool specification

Tool Information:

  • Name: TopDB_get_topology

  • Type: TopDBTool

  • Description: Retrieve experimentally curated transmembrane topology for a protein from TopDB. Returns each sequence region labelled Membrane, Inside or Outside with its residue range, the number of transmembrane regions, a reliability score, and the underlying experimental evidence records. Use this to check a sequence-based prediction from EBI_predict_membrane_topology against curated experimental data. Example: identifier=’P02699’ (bovine rhodopsin, seven transmembrane helices).

Parameters:

  • identifier (string) (required) UniProt accession such as ‘P02699’, or a TopDB entry name such as ‘OPSD_BOVIN’.

Example Usage:

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