Skills pdb-database

🧬

pdb-database

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

Safe ⚙️ External commands🌐 Network access📁 Filesystem access

Search Protein Data Bank for molecular structures

Also available from: davila7

Access the RCSB Protein Data Bank to search for and download 3D structures of proteins and nucleic acids. This skill enables structural biology research, drug discovery, and protein engineering by providing programmatic access to over 200,000 experimentally determined and computationally modeled molecular structures.

Supports: Claude Codex Code(CC)

⚠️ 68 Poor

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Test it

Using "pdb-database". Find structures similar to human hemoglobin

Expected outcome:

Found 5 similar structures:
- 4HHB - Hemoglobin (1.74 Å, X-RAY DIFFRACTION, Homo sapiens)
- 1HHO - Hemoglobin (2.10 Å, X-RAY DIFFRACTION, Pan troglodytes)
- 1A3N - Hemoglobin (2.50 Å, X-RAY DIFFRACTION, Equus caballus)
Resolution range: 1.74 - 3.20 Å

Security Audit

Safe

v4 • 1/17/2026

This is a legitimate scientific skill for accessing the public RCSB Protein Data Bank. All 232 static findings are false positives. The scanner misinterpreted markdown inline code formatting (backticks) as Ruby shell execution, protein amino acid sequences as Windows SAM database, generic substrings as cryptographic algorithms, and public scientific API endpoints as network threats.

Files scanned

927

Lines analyzed

findings

Total audits

Risk Factors

⚙️ External commands (115)

🌐 Network access (49)

📁 Filesystem access (3)

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

Audited by: claude View Audit History →

Quality Score

Architecture

100

Maintainability

Content

Community

100

Security

Spec Compliance

What You Can Build

Find drug-target complexes

Search for protein-ligand complexes to understand binding sites and design new therapeutics.

Compare mutant structures

Find homologous structures and analyze sequence-structure relationships for protein design.

Download structures for analysis

Retrieve 3D coordinates for computational analysis, visualization, and structure-based research.

Try These Prompts

Basic structure search

Find the PDB entry for hemoglobin and tell me its resolution and experimental method.

Sequence search

Find proteins with sequences similar to: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVID

Filter by quality

Find all human protein structures with resolution better than 2.0 Angstroms determined by X-ray crystallography.

Batch download

Download the PDB files for entries 4HHB, 1MBN, and 1GZX in mmCIF format.

Best Practices

Use the Search API to get PDB IDs first, then fetch detailed data to minimize API calls.
Implement rate limiting with delays between requests to avoid hitting API limits.
Cache frequently accessed data locally to reduce redundant network requests.

Avoid

Making individual API calls in a loop without delays - this will trigger rate limits.
Downloading entire database when only specific entries are needed.
Not checking API response status codes before processing data.

Frequently Asked Questions

What is the difference between PDB and mmCIF formats?

PDB is the legacy text format with column constraints. mmCIF is the modern standard that handles larger structures and more metadata.

How do I parse downloaded structure files?

Use BioPython's PDBParser for PDB files or the mmCIF parser for mmCIF format. Both can iterate through atoms and residues.

What is a good resolution for crystal structures?

High-resolution structures are below 2.0 Å. Structures between 2.0-3.0 Å are moderate quality. Above 3.0 Å is lower resolution.

How do I search by protein sequence?

Use SequenceQuery with your amino acid sequence. Set evalue_cutoff and identity_cutoff to filter results by similarity.

What are biological assemblies?

Biological assemblies represent the functional form of a macromolecule, which may differ from the crystallographic asymmetric unit.

Can I search for ligand-bound structures?

Yes, use AttributeQuery with rcsb_nonpolymer_entity_instance_container_identifiers.comp_id to find structures containing specific ligands like ATP or heme.

Developer Details

Author

K-Dense-AI

License

MIT

Repository

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

Ref

main

File structure

📁 references/

📄 api_reference.md

📄 evaluation_result.json

📄 SKILL.md