Structure Annotation Tools¶

Configuration File: structure_annotation_tools.json Tool Type: Local Tools Count: 1

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

Available Tools¶

Per-residue structural annotation from a PDB structure: which residues sit at a binding interface…

Structure_annotate_per_residue tool specification

Tool Information:

Name: Structure_annotate_per_residue
Type: StructureAnnotationTool
Description: Per-residue structural annotation from a PDB structure: which residues sit at a binding interface (vs a partner chain), which line a ligand pocket, which are buried (core) vs solvent-exposed (surface). For each residue of the target chain returns: 1-letter amino acid, min side-chain-heavy-atom distance to the partner chain(s), min distance to ligand heavy atoms, relative SASA (computed with freesasa on the ISOLATED target chain — partner chains would bias the call by burying interface residues), a region label in {interface, ligand, both, other}, and an is_core boolean. Optionally fetches secondary structure (helix/strand/coil) from PDBe REST. This is the structural annotation track plotted under a DMS heatmap and the structural prior SAE feature drops are read against. Methodology adapted from an upstream research workflow.

Parameters:

operation (string) (required) Operation type
pdb_id ([‘string’, ‘null’]) (optional) 4-character PDB ID (e.g. ‘6VJJ’). If provided, the structure is downloaded from RCSB. Exactly one of pdb_id or pdb_content must be supplied.
pdb_content ([‘string’, ‘null’]) (optional) Raw PDB file content (string). Use when the structure is local (e.g. AlphaFold-predicted, in-memory).
target_chain (string) (optional) Chain ID of the protein to annotate (e.g. ‘A’).
partner_chains (array) (optional) Chain IDs that define the binding partner(s). Used to compute the interface. Empty list = no interface analysis (all dist_partner values null).
ligand_resnames (array) (optional) Three-letter residue names of bound ligands to define the ligand pocket (e.g. [‘GNP’, ‘MG’] for GTP-analogue + magnesium). Searched across all chains. Empty list = no ligand-pocket analysis.
distance_cutoff (number) (optional) Distance cutoff in angstroms for interface and ligand-pocket classification.
core_rsa_cutoff (number) (optional) Relative solvent accessibility threshold below which a residue is classified as ‘core’.
include_secondary_structure (boolean) (optional) If true and pdb_id is provided, fetch per-residue secondary structure (helix/strand/coil) from PDBe REST. Only meaningful for deposited PDB entries; ignored when pdb_content is supplied.

Example Usage:

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