Rcsb pdb search

Skill ma-compbio-lab/SkillFoundry/skills/structural-biology/rcsb-pdb-search

Use this skill to search the Protein Data Bank through the official RCSB Search API when you need structure identifiers from a free-text query. Do not use it when you need structure download or coordinate parsing.From its SKILL.md

Install

npx -y skills add ma-compbio-lab/SkillFoundry --skill rcsb-pdb-search

Assembled from the repository path, not quoted from the project. Check it against their README if it does not work.

SKILL.md

1.5 KB, 327 tokens by cl100k_base, as published. Nobody here has run it

Purpose

Run lightweight RCSB PDB entry searches and save the result set as JSON.

When to use

You need a quick structure search from a protein, ligand, or concept keyword.
You want PDB entry IDs for downstream structural analysis.

When not to use

You need mmCIF/PDB coordinate files.
You need local structural parsing rather than remote search.

Inputs

Query string
Optional --rows and --out

Outputs

Search API JSON containing PDB entry identifiers

Requirements

Python 3.13+
Network access to search.rcsb.org

Procedure

Run python3 skills/structural-biology/rcsb-pdb-search/scripts/search_rcsb.py --query hemoglobin --rows 3 --out skills/structural-biology/rcsb-pdb-search/assets/hemoglobin_results.json.
Review total_count and result_set.

Validation

Command exits successfully.
Output JSON contains result_set.
At least one structure ID is returned for a common query.

Failure modes and fixes

Empty results: broaden the text query.
HTTP errors: retry later or reduce result count.

Safety and limits

This is a metadata search skill, not a molecular modeling workflow.

Examples

python3 .../search_rcsb.py --query "p53" --rows 2

Provenance

RCSB Search API docs: https://search.rcsb.org/

Related skills

ensembl-gene-lookup

What ships with it: 7 files

3.2 KB alongside SKILL.md, 1 of them executable