rcsb-pdb-search 100/100

Is rcsb-pdb-search safe to install?

SaferSkills independently audited rcsb-pdb-search (Agent Skill) and scored it 100/100 (green). The audit ran 55 deterministic rules across Security, Supply Chain, Maintenance, Transparency, and Community; it found 0 high-severity and 0 lower-severity findings. The full rule-by-rule trace and per-finding evidence are below. Free, methodology-open.

CategoryWeightCategory scoreContribution

Securityprompt, exec, net, exfil, eval

35%

100

35.0 pts

Supply chainhash, typosquat, maintainer, lockfile

20%

100

20.0 pts

Maintenancestaleness, pinning, CI

15%

100

15.0 pts

TransparencySKILL.md, perms, README

15%

100

15.0 pts

Communityinstalls, verify, response

15%

100

15.0 pts

Findings & checks · 0 flagged

Securityscore 100 · 0 findings

✓—All security checks passedNo findings in this category for the latest scan.pass

Supply chainscore 100 · 0 findings

✓—All supply chain checks passedNo findings in this category for the latest scan.pass

Maintenancescore 100 · 0 findings

✓—All maintenance checks passedNo findings in this category for the latest scan.pass

Transparencyscore 100 · 0 findings

✓—All transparency checks passedNo findings in this category for the latest scan.pass

Communityscore 100 · 0 findings

✓—All community checks passedNo findings in this category for the latest scan.pass

The primary manifest — the file an agent reads to learn what this artifact does.

skills/structural-biology/rcsb-pdb-search/SKILL.md · 1 file

skills/structural-biology/rcsb-pdb-search/SKILL.md1.5 KB · Markdown

name: rcsb-pdb-search

description: 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.

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/

ensembl-gene-lookup

rcsb-pdb-search— agent skill

Is rcsb-pdb-search safe to install?

Purpose

When to use

When not to use

Inputs

Outputs

Requirements

Procedure

Validation

Failure modes and fixes

Safety and limits

Examples

Provenance

Audit the pieces. Scan the whole. Decide.

Is rcsb-pdb-search safe to install?

Purpose

When to use

When not to use

Inputs

Outputs

Requirements

Procedure

Validation

Failure modes and fixes

Safety and limits

Examples

Provenance

Related skills

Audit the pieces. Scan the whole. Decide.