What file formats does the PDB Database skill support?

The skill supports downloading structure coordinates in PDB, mmCIF, and BinaryCIF formats, as well as specific biological assemblies.

Does this skill require specific Python packages?

Yes, it is designed to work with the 'rcsb-api' package, which provides unified access to both Search and Data APIs.

Can I filter protein structures by their experimental resolution?

Absolutely. You can use AttributeQuery to filter results by resolution, experimental method (e.g., X-ray diffraction, Cryo-EM), and organism source.

Can I search for proteins using a raw amino acid sequence?

Yes, the skill includes SequenceQuery capabilities which allow you to find structures based on sequence identity and e-value cutoffs.

Does this skill provide access to AlphaFold models?

Yes, it can retrieve and process computed structure models from AlphaFold and ModelArchive using their respective prefixes within the PDB ecosystem.

RCSB PDB Database Access

Name: RCSB PDB Database Access
Author: K-Dense-AI

byK-Dense-AI

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2,188

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Data Science & ML

Enables programmatic access to the RCSB Protein Data Bank for searching, retrieving, and analyzing 3D structures of biological macromolecules.

This skill integrates the RCSB PDB database into the Claude Code environment, allowing researchers and developers to perform complex searches for protein and nucleic acid structures using text, sequence identity, or structural similarity. It streamlines workflows for structural biology and drug discovery by providing direct methods to download coordinate files in PDB or mmCIF formats, fetch detailed experimental metadata via GraphQL, and perform efficient batch operations using the official RCSB Python API. Whether you are identifying drug targets or building bioinformatics pipelines, this skill provides the necessary tools for deep structural data integration.

Key Features

01Automated coordinate file downloads in PDB, mmCIF, and BinaryCIF formats

022,188 GitHub stars

03Advanced search by text, sequence identity, and 3D structural geometry

04Metadata retrieval using flexible GraphQL queries and predefined schemas

05Direct integration with structural analysis libraries like BioPython

06Batch processing capabilities for handling multiple PDB entries simultaneously

Use Cases

01Automating data collection for structural biology research and large-scale bioinformatics pipelines

02Retrieving high-resolution homologous structures for comparative protein modeling and engineering

03Identifying drug targets by searching for specific protein-ligand complexes and binding sites

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add k-dense-ai/claude-scientific-skills pdb-database

For use in Claude.ai and ChatGPT

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