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structure-pocket-inspection

Inspect PDB structures and identify protein residues near a ligand or pocket center.

64|15|Updated Aug 14, 2026
Search Tags:#python#protein structure#pdb#structural biology#ligand#binding pocket#residue analysis
One-click install
npx skills add https://github.com/openJiuwen-ai/sciencediscovery --skill structure-pocket-inspection-openjiuwen-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: structure-pocket-inspection
Source: https://github.com/openJiuwen-ai/sciencediscovery/tree/main/skills/structure-pocket-inspection
Command: npx skills add https://github.com/openJiuwen-ai/sciencediscovery --skill structure-pocket-inspection-openjiuwen-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes scripts (resource) components.

What problem does it solve? Researchers need a transparent, reproducible first-pass view of a local PDB structure before committing to heavier modeling. This Skill summarizes chains and residue composition and lists protein atoms within a chosen distance of a ligand or pocket center, without predicting affinity or docking poses. ## Core Features & Use Cases - Structure Summarization: Parses ATOM and HETATM records to report chain counts, residue composition, atom totals, and malformed records. - Pocket Proximity Analysis: Finds protein residues within a user-defined cutoff (up to 25 Å) of a named ligand residue or an explicit Cartesian pocket center. - Provenance-Friendly Output: Writes a JSON result capturing input, target, cutoff, and nearby residues so runs are traceable. - Use Case: Given a crystal structure with a bound ATP, list every protein residue within 5 Å of the ligand to draft a candidate binding-site residue list before docking or mutagenesis studies. ## Quick Start Ask the assistant to inspect your local structure.pdb file and report all protein residues within 5 angstroms of the ATP ligand, saving the result as pocket.json.

Frequently Asked Questions about structure-pocket-inspection

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

FAQPage Schema
How do I find residues near a ligand in a PDB file?▼

Run the bundled inspect_pdb.py script with the PDB path, the ligand residue name via --ligand, and a distance cutoff in angstroms. It writes a JSON file listing nearby protein residues sorted by nearest distance.

How do I inspect a binding pocket without a known ligand?▼

Pass the pocket center as three Cartesian coordinates with --center X Y Z instead of a ligand name. The script then reports protein residues within the cutoff distance of that point.

Does this PDB inspection require external Python packages?▼

No, the script uses only the Python 3 standard library (argparse, json, math, pathlib). It runs on any local PDB file in an authorized workspace without installing dependencies.

Can proximity analysis predict binding affinity or docking poses?▼

No, geometric proximity is not evidence of binding, catalysis, or docking quality. This inspection only reports observed coordinates and nearby residues as a first-pass structural summary.

How are alternate locations and multiple models handled in PDB parsing?▼

The script analyzes only the first model, stopping at the first ENDMDL record, and keeps atoms with blank or A alternate location identifiers. Malformed ATOM or HETATM records are counted and reported rather than guessed.

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