Channelsdb Tools

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

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

Available Tools

ChannelsDB_get_channels_cofactor (Type: BaseRESTTool)

Get cofactor access tunnel data for a PDB structure from ChannelsDB. Specifically detects tunnels…

ChannelsDB_get_channels_cofactor tool specification

Tool Information:

  • Name: ChannelsDB_get_channels_cofactor

  • Type: BaseRESTTool

  • Description: Get cofactor access tunnel data for a PDB structure from ChannelsDB. Specifically detects tunnels that provide access pathways for cofactors and small molecules to reach enzyme active sites or binding pockets. Each channel includes geometric profile data (radius along the path, 3D coordinates), physicochemical properties (charge, hydrophobicity, polarity), and the residue layers that line the tunnel. Use ChannelsDB_get_channels_pdb for a complete view of all channel types including transmembrane pores and reviewed channels.

Parameters:

  • pdb_id (string) (required) PDB structure identifier (4-character code). Examples: ‘5i6x’ (MscL), ‘3sn6’ (GPCR-Gs complex).

Example Usage:

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

ChannelsDB_get_channels_pdb (Type: BaseRESTTool)

Get protein channel, tunnel, and pore data for a PDB structure from ChannelsDB. ChannelsDB is a c…

ChannelsDB_get_channels_pdb tool specification

Tool Information:

  • Name: ChannelsDB_get_channels_pdb

  • Type: BaseRESTTool

  • Description: Get protein channel, tunnel, and pore data for a PDB structure from ChannelsDB. ChannelsDB is a comprehensive database of channels (tunnels, pores, and voids) found in biomacromolecular structures deposited in the Protein Data Bank. Returns channel geometry profiles (radius, distance along path, 3D coordinates), physicochemical properties (charge, hydrophobicity, polarity, mutability), residue layers lining each channel, and expert annotations when available. Useful for studying transport pathways in membrane proteins, enzyme active site access tunnels, and ion channels. Example: get channels for aquaporin structure 1ymg or hemoglobin 4hhb.

Parameters:

  • pdb_id (string) (required) PDB structure identifier (4-character code, case-insensitive). Examples: ‘1ymg’ (aquaporin), ‘3sn6’ (beta2-adrenergic receptor-Gs complex), ‘4hhb’ (hemoglobin), ‘5i6x’ (MscL mechanosensitive channel).

Example Usage:

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