Skills pdb-database

📦

pdb-database

Name: pdb-database
Author: K-Dense-AI

Content revision r1 Safe ⚙️ External commands🌐 Network access📁 Filesystem access

Search PDB Structures for Research

Structural biology work often requires fast access to public protein and nucleic acid structures. This skill helps Claude, Codex, and Claude Code search RCSB PDB, retrieve metadata, and download coordinate files.

Supports: Claude Codex Code(CC)

📊 73 Adequate

Install with my Agent

Copy this request to your Agent. It includes the canonical Skill page and manifest.

Agent request

Review the Skillstore skill "pdb-database" from https://skillstore.io/skills/k-dense-ai-pdb-database.md and its manifest at https://skillstore.io/api/skills/k-dense-ai-pdb-database/manifest. Verify the artifact. You may proceed after verification, subject to the environment's own policy.

Your Agent should still show its plan and request any confirmation required by the security policy.

Agent-readable resources

Use these links when an AI agent, crawler, or script needs clean context instead of reading the full page.

Markdown detail GET /skills/k-dense-ai-pdb-database.md Signed manifest GET /api/skills/k-dense-ai-pdb-database/manifest Signed lockfile GET /api/skills/k-dense-ai-pdb-database/lockfile

Test it

Using "pdb-database". Find human hemoglobin structures with good resolution.

Expected outcome:

A suitable result is 4HHB, human deoxyhemoglobin, solved by X-ray diffraction at 1.74 Angstrom resolution.
Other related entries may be useful for ligand state or mutation comparisons.
Use mmCIF format for modern downstream analysis.

Using "pdb-database". Download coordinates for 1MBN and explain what I received.

Expected outcome:

The skill can retrieve the coordinate file from the public RCSB download service.
The result is a structure file containing atomic coordinates for myoglobin.
Use BioPython, PyMOL, ChimeraX, or similar tools for visualization and atom-level analysis.

Using "pdb-database". Compare PDB and mmCIF formats.

Expected outcome:

PDB is the older fixed-column format. mmCIF is the modern standard and is better for large structures and richer metadata.

Security Audit

Safe

v9 • 7/9/2026 Open versioned report

The static findings are false positives from markdown examples, public RCSB PDB API URLs, safe file-download examples, and scientific terminology. I found no prompt injection, credential access, destructive behavior, data exfiltration, or hidden execution intent in the reviewed files.

Files scanned

1,140

Lines analyzed

Review items

False positives ignored

Risk Factors

⚙️ External commands (33)

🌐 Network access (39)

📁 Filesystem access (3)

references/api_reference.md:407 SKILL.md:159 SKILL.md:165

No confirmed security findings were detected by the latest completed static and semantic audit. This does not prove the skill has no side effects.

Audited by: claude View Audit History →

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Open versioned report

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https://skillstore.io/skills/k-dense-ai-pdb-database/audits/9?utm_source=security_passport&utm_medium=share&utm_campaign=versioned_report

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Academic citations (APA · BibTeX · CFF)

APA citation

K-Dense-AI. (2026). pdb-database security audit report (audit version 9) [Author version unspecified]. Skillstore. https://skillstore.io/skills/k-dense-ai-pdb-database/audits/9

BibTeX citation

@techreport{k-dense-ai-k-dense-ai-pdb-database-2026,
  author = {K-Dense-AI},
  title = {pdb-database security audit report (audit version 9)},
  institution = {Skillstore},
  year = {2026},
  number = {9},
  url = {https://skillstore.io/skills/k-dense-ai-pdb-database/audits/9},
  note = {Author version unspecified}
}

CITATION.cff

cff-version: 1.2.0
message: "If you use this Skill, cite its author and this versioned security audit report."
title: "pdb-database security audit report (audit version 9)"
version: "unspecified"
type: report
authors:
  - name: "K-Dense-AI"
date-released: "2026-07-09"
url: "https://skillstore.io/skills/k-dense-ai-pdb-database/audits/9"
identifiers:
  - type: other
    value: "skillstore:k-dense-ai-pdb-database:audit:9"
    description: "Skillstore immutable audit report identifier"

Compare variants

2 installable variants

Each author remains a separate installable skill. The recommended variant is ranked by Skillstore evidence.

Why this variant is first

Highest Skillstore Score

Author / source Skillstore Score Evidence Confidence Skillstore usage Updated

davila7 Recommended

davila7-pdb-database

Skillstore Score 74

Evidence Confidence High

Skillstore usage 9

Updated

2026-08-21

K-Dense-AI Current

k-dense-ai-pdb-database

Skillstore Score 73

Evidence Confidence High

Skillstore usage 9

Updated

2026-08-21

Skillstore Score

Why this score Evidence Confidence: High

Architecture

Maintainability

Content

Community

Spec Compliance

What You Can Build

Retrieve structures for analysis

Find high-quality entries, inspect experimental metadata, and download coordinates for computational workflows.

Identify target and ligand structures

Search for protein targets, ligand-bound complexes, and related structures for binding-site review.

Compare homologous structures

Use sequence and structural similarity searches to find templates for design, modeling, and mutation analysis.

Try These Prompts

Find a known protein

Find RCSB PDB structures for hemoglobin and summarize the best entry, resolution, organism, and experimental method.

Search by sequence

Search for PDB structures similar to this protein sequence and rank the top matches by identity and resolution: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVID.

Filter high-quality entries

Find human kinase structures solved by X-ray crystallography with resolution better than 2.0 Angstroms and list useful PDB IDs.

Build a batch workflow

For PDB IDs 4HHB, 1MBN, and 1GZX, retrieve metadata, download mmCIF files, and summarize method, resolution, organism, and file names.

Best Practices

Use search queries to narrow PDB IDs before downloading coordinate files.
Respect API rate limits by batching requests and adding delays for large jobs.
Prefer mmCIF for modern structural biology workflows and large assemblies.

Avoid

Do not download large sets of structures without filtering and rate limiting.
Do not assume every PDB entry has high resolution or complete metadata.
Do not use downloaded coordinate files without checking experimental method and quality metrics.

Frequently Asked Questions

What databases does this skill use?

It uses public RCSB Protein Data Bank APIs and download endpoints for structures, metadata, and sequences.

Can it search by protein sequence?

Yes. It describes SequenceQuery workflows for protein, DNA, or RNA sequence similarity searches.

Can it download structure files?

Yes. It provides guidance for downloading PDB, mmCIF, structure factor, and biological assembly files.

What is the difference between PDB and mmCIF?

PDB is a legacy text format. mmCIF is the modern format with better support for large structures and metadata.

Does it analyze molecular geometry directly?

It helps retrieve and prepare data. Detailed coordinate analysis usually requires tools such as BioPython or molecular viewers.

Is an API key required?

No API key is described for the public RCSB endpoints covered by this skill.

Developer Details

Author

K-Dense-AI

License

Unknown

Skillstore revision

Version notice

The author did not declare a version.

Repository

https://github.com/K-Dense-AI/claude-scientific-skills/tree/main/scientific-skills/pdb-database

Ref

1ffa7643651792ccb4bd3b15d924d2c97edff755

Maintenance freshness

7/18/2026

Usage

7 downloads · 484 views

File structure

📁 references/

📄 api_reference.md

📄 evaluation_result.json

📄 SKILL.md

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pdb-database

Install with my Agent

Agent-readable resources

Test it

Security Audit

Risk Factors

Copy report link

Markdown badge

HTML badge

Embed card

APA citation

BibTeX citation

CITATION.cff

Compare variants

Skillstore Score

What You Can Build

Retrieve structures for analysis

Identify target and ligand structures

Compare homologous structures

Try These Prompts

Best Practices

Avoid

Frequently Asked Questions

Developer Details

More from K-Dense-AI

venue-templates

iso-13485-certification

pytdc

diffdock

statistical-analysis

scanpy

Related Skills

bioservices

nature-reviewer

drugbank-database

kegg-database

deep-research

tavily-web