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tooluniverse-protein-structural-annotation-pdb

Annotate per-residue interface, ligand-pocket, and burial status from PDB structures.

1.7k|254|Updated Mar 3, 2025
Search Tags:#protein structure#pdb#DMs#structural biology#ligand pocket#binding interface#residue annotation
One-click install
npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-protein-structural-annotation-pdb
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: tooluniverse-protein-structural-annotation-pdb
Source: https://github.com/mims-harvard/ToolUniverse/tree/main/plugins/tooluniverse/skills/tooluniverse-protein-structural-annotation-pdb
Command: npx skills add https://github.com/mims-harvard/ToolUniverse --skill tooluniverse-protein-structural-annotation-pdb

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Interpreting variants or DMS (deep mutational scanning) results requires knowing each residue's physical context, but manually computing which residues sit at binding interfaces, line ligand pockets, or are buried in the core is tedious and error-prone, especially given PDB numbering offsets.

Core Features & Use Cases

  • Per-Residue Structural Annotation: Classifies every residue of a target chain as interface, ligand-pocket, both, or other, plus buried (core) vs solvent-exposed via relative solvent accessibility.
  • Structure Discovery & Numbering Verification: Finds the right PDB entry from a UniProt accession via PDBe SIFTS or RCSB search, and verifies residue numbering against canonical UniProt sequences using landmark residues.
  • Use Case: Given KRAS structure 6VJJ, produce a 168-row annotation table marking which residues contact the RAF1 partner chain and the GNP ligand, then use it as the structural track under a DMS heatmap to interpret variant effects.

Quick Start

Annotate each residue of chain A in PDB 6VJJ for interface contacts with chain B, proximity to ligands GNP and MG, and core versus surface burial.

Frequently Asked Questions about tooluniverse-protein-structural-annotation-pdb

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I annotate which residues are at a protein binding interface?▼

Run the per-residue annotation with a PDB ID, target chain, and partner chains; residues within the distance cutoff (default 5.0 Å) of a partner chain are labeled as interface residues. The output includes per-residue distances, region labels, and burial status.

How to find the right PDB structure for a UniProt accession?▼

Use PDBe SIFTS best-structures lookup with the UniProt accession to get a ranked list of PDB IDs by coverage and resolution. Alternatively, use RCSB advanced search for free-text queries when no UniProt accession is available.

Why do PDB residue numbers not match UniProt positions?▼

Crystal constructs add N-terminal cloning tags or skip disordered termini, creating silent numbering offsets. Always verify with a landmark residue, such as checking that KRAS position 12 is glycine, and record the offset explicitly before joining data.

Can this detect pockets without a known ligand?▼

No, ligand-pocket annotation requires specified ligand residue names present as HETATM records in the structure. For de novo pocket detection without a known ligand, use docking tools or PDBe pre-computed pockets instead.

What are the limitations of single-structure residue annotation?▼

A static crystal structure captures one conformer, so interface or pocket assignments may differ in alternative conformations. The 5.0 Å distance cutoff is a convention, and modified residues within the chain are not detected as ligands.

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