Can I search for structures by protein sequence?

Yes, the skill supports Sequence Similarity searches using the RCSB Search API, allowing you to find homologous structures with customizable identity and E-value cutoffs.

Does this skill support AlphaFold models?

Yes, it provides access to the RCSB PDB repository which includes both experimentally determined structures and computed models such as those from AlphaFold and ModelArchive.

What data formats can I download with this skill?

You can download structural coordinates in PDB, mmCIF (PDBx), and BinaryCIF formats, as well as biological assemblies and experimental metadata.

Do I need an API key to use the PDB Database skill?

No, the RCSB PDB APIs are public and do not require an API key for standard usage, making it easy to integrate into your Claude Code workflows.

Can I perform complex multi-criteria searches?

Absolutely. You can use logical operators (AND/OR) to combine text, attribute, sequence, and structural similarity queries to find very specific biological entries.

PDB Database

Name: PDB Database
Author: Sologa

bySologa

0•

データサイエンスとML

Accesses and manages 3D biological macromolecular structures from the RCSB Protein Data Bank for structural biology and drug discovery.

This skill provides a programmatic interface to the RCSB Protein Data Bank (PDB), the global repository for 3D structural data of proteins and nucleic acids. It enables researchers and developers to search for structures using text, sequence, or structural similarity, retrieve detailed metadata via GraphQL, and download coordinate files in various formats like PDB and mmCIF. Ideal for structural biology, drug discovery, and protein engineering, it streamlines the integration of experimental and computed structural models into automated computational workflows.

主な機能

01Multi-format coordinate downloads including PDB, mmCIF, and BinaryCIF

02Flexible data retrieval using the RCSB Data API and GraphQL

030 GitHub stars

04Advanced search by text, sequence similarity, and 3D geometry

05Batch processing capabilities for large-scale structural analysis

06Access to 200,000+ experimentally determined and computed models

ユースケース

01Integrating structural metadata into bioinformatics pipelines and research reports

02Building datasets for machine learning models in protein folding or design

03Automating drug target identification and ligand binding site analysis

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add sologa/codex-pipeline pdb-database

For use in Claude.ai and ChatGPT