Which Python packages are required?

The skill primarily utilizes the 'rcsb-api' package for data access and 'BioPython' for parsing and structural analysis.

Can I search for structures using a protein sequence?

Yes, the skill supports sequence similarity searches where you can define e-value and identity cutoffs to find homologous structures and templates.

Does this skill support AlphaFold models?

Yes, it can access computed structure models from AlphaFold and ModelArchive using their specific entry prefixes (e.g., AF_ or MA_) available through the RCSB API.

Can I perform batch operations with this skill?

Absolutely. The skill is designed to handle multiple PDB IDs efficiently, allowing for automated metadata extraction and coordinate downloads across large datasets.

What formats can I download structures in?

You can download coordinates in the legacy PDB format, the modern mmCIF standard, and BinaryCIF for efficient data transfer and large-scale processing.

PDB Structural Biology Database

Name: PDB Structural Biology Database
Author: Zehong-Wang

byZehong-Wang

0•

データサイエンスとML

Accesses and retrieves 3D protein and nucleic acid structures from the RCSB PDB for structural biology and drug discovery research.

The PDB Database skill enables Claude to interact directly with the RCSB Protein Data Bank, the global repository for biological macromolecular structures. It provides comprehensive tools for searching structures via text, sequence similarity, or 3D geometry, and facilitates the retrieval of atomic coordinates and rich metadata. This skill is essential for researchers and developers working in bioinformatics, drug discovery, and protein engineering who need to integrate high-quality structural data into their computational workflows or AI-driven analysis.

主な機能

01Automated downloading of coordinate files in PDB, mmCIF, and BinaryCIF formats

02Advanced search by text, sequence identity, and 3D structural similarity

030 GitHub stars

04Flexible data retrieval via REST and GraphQL for metadata and experimental details

05Batch processing capabilities for large-scale structural analysis

06Integration with BioPython for parsing and analyzing structural geometry

ユースケース

01Automating drug target identification by searching for specific protein-ligand complexes

02Extracting experimental metadata and quality metrics for structural validation

03Building datasets for machine learning models in protein folding or design

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add zehong-wang/kosmos pdb-database

For use in Claude.ai and ChatGPT

Download Skill