Pdbepisa Tools

Configuration File: pdbepisa_tools.json Tool Type: Local Tools Count: 3

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

Available Tools

PDBePISA_get_assemblies (Type: PDBePISATool)

Get predicted biological assemblies from a crystal structure using PDBePISA. Analyzes crystal pac…

PDBePISA_get_assemblies tool specification

Tool Information:

  • Name: PDBePISA_get_assemblies

  • Type: PDBePISATool

  • Description: Get predicted biological assemblies from a crystal structure using PDBePISA. Analyzes crystal packing to predict the most likely biological assembly (monomer, dimer, tetramer, etc.) with stability scores, dissociation energy, accessible/buried surface areas, and composition. Use after structure retrieval from RCSB/PDBe to determine the biologically relevant oligomeric state. Positive dissociation energy indicates a stable assembly.

Parameters:

  • pdb_id (string) (required) PDB entry ID (4-character code, e.g., ‘4hhb’ for hemoglobin tetramer, ‘3hl2’ for insulin dimer)

Example Usage:

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

PDBePISA_get_interfaces (Type: PDBePISATool)

Analyze protein-protein and protein-ligand interfaces in a crystal structure using PDBePISA. Retu…

PDBePISA_get_interfaces tool specification

Tool Information:

  • Name: PDBePISA_get_interfaces

  • Type: PDBePISATool

  • Description: Analyze protein-protein and protein-ligand interfaces in a crystal structure using PDBePISA. Returns interface area, solvation energy, p-value, hydrogen bonds, salt bridges, disulfide bonds, and per-molecule contributions for each interface. Use after retrieving a PDB structure from RCSB/PDBe tools to assess biological relevance of crystal contacts. Low p-value (<0.5) and negative solvation energy suggest biologically relevant interfaces.

Parameters:

  • pdb_id (string) (required) PDB entry ID (4-character code, e.g., ‘4hhb’ for hemoglobin, ‘1cbs’ for CRABP-II)

Example Usage:

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

PDBePISA_get_monomer_analysis (Type: PDBePISATool)

Analyze solvent-accessible surface area and interface participation for each chain in a PDB struc…

PDBePISA_get_monomer_analysis tool specification

Tool Information:

  • Name: PDBePISA_get_monomer_analysis

  • Type: PDBePISATool

  • Description: Analyze solvent-accessible surface area and interface participation for each chain in a PDB structure using PDBePISA. Returns per-chain total interface area, number of interface contacts, and detailed interface participations. Useful for identifying which chains are most involved in crystal contacts and protein interactions. Use with RCSB/PDBe structure data and STRING network analysis.

Parameters:

  • pdb_id (string) (required) PDB entry ID (4-character code, e.g., ‘4hhb’ for hemoglobin, ‘1cbs’ for CRABP-II)

Example Usage:

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