What data formats does the PDB Database skill support?

The skill supports downloading and processing coordinates in PDB, mmCIF, and BinaryCIF formats, as well as retrieving metadata via JSON and GraphQL.

Can I search for structures using a protein sequence?

Yes, the skill includes built-in capabilities to perform sequence similarity searches with customizable identity and e-value cutoffs to find homologous structures.

Is this skill compatible with AlphaFold models?

Yes, it can access computed models available through the RCSB PDB, including entries with AF_ (AlphaFold) and MA_ (ModelArchive) prefixes.

How do I install the necessary dependencies for this skill?

You should install the official client using 'uv pip install rcsb-api' to enable all search and data retrieval features within your Claude environment.

PDB Structure Database

Name: PDB Structure Database
Author: Yezez9

byYezez9

0•

データサイエンスとML

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

The PDB Database skill enables Claude to interact seamlessly with the RCSB Protein Data Bank, the global repository for 3D structural data of proteins and nucleic acids. It allows researchers and developers to perform complex searches by text, sequence similarity, or structural geometry, retrieve detailed metadata via GraphQL, and download coordinate files in PDB or mmCIF formats. This skill is essential for bioinformatics workflows, drug target identification, and protein engineering projects that require programmatic access to experimental and computational structural models.

主な機能

01Metadata retrieval using flexible GraphQL and REST queries

020 GitHub stars

03Advanced structural searching by sequence similarity and 3D geometry

04Automated downloading of PDB, mmCIF, and BinaryCIF coordinate files

05Batch processing of multiple PDB entries for high-throughput analysis

06Integration with BioPython for coordinate parsing and structural analysis

ユースケース

01Identifying drug targets by searching for specific protein-ligand binding sites

02Automating data collection for structural biology research and publications

03Building datasets for machine learning models in protein folding and engineering

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add yezez9/research-agent pdb-database

For use in Claude.ai and ChatGPT