What is the RCSB PDB?

The RCSB Protein Data Bank (PDB) is the global repository for 3D structural data of biological macromolecules, including proteins and nucleic acids.

What Python libraries are required?

The skill primarily uses the 'rcsb-api' package. It also integrates well with BioPython for parsing and analyzing the downloaded coordinate files.

Can I search for structures using a protein sequence?

Yes, the skill includes SequenceQuery capabilities, allowing you to find structures by sequence similarity with specific E-value and identity cutoffs.

Which coordinate file formats can I download?

This skill supports downloading structures in modern mmCIF, legacy PDB, and compressed BinaryCIF formats.

Does this skill support AlphaFold models?

Yes, it can access computed structure models, including AlphaFold entries, which typically use the 'AF_' prefix.

PDB Database Structural Biology

Name: PDB Database Structural Biology
Author: ricable

byricable

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データサイエンスとML

Accesses and analyzes 3D protein and nucleic acid structures from the RCSB Protein Data Bank for research and discovery.

The PDB Database skill enables Claude to programmatically interact with the RCSB PDB, the global repository for macromolecular structural data. It provides comprehensive capabilities for searching over 200,000 structures by text, sequence, or 3D geometry, downloading coordinate files in modern mmCIF or legacy PDB formats, and extracting rich metadata. This skill is essential for structural biologists and bioinformaticians working on drug discovery, protein engineering, and computational biology workflows within the Claude Code environment.

主な機能

011 GitHub stars

02Automated coordinate file downloads in PDB, mmCIF, and BinaryCIF formats

03Advanced structure searching by text, attribute, sequence, and 3D geometry

04Batch processing and metadata extraction for multiple entries

05Flexible data retrieval via GraphQL and standard Python APIs

06Seamless integration with structural biology libraries like BioPython

ユースケース

01Automating the collection of high-resolution structural datasets for machine learning

02Finding homologous structures for protein engineering and homology modeling

03Identifying drug targets and analyzing ligand binding sites for pharmaceutical research

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add ricable/ultimate-ai-agent pdb-database

For use in Claude.ai and ChatGPT

Download Skill