Can this skill search for structures by amino acid sequence?

Yes, it supports SequenceQuery which finds structures based on sequence similarity, allowing you to specify identity and e-value cutoffs.

Can I perform complex queries like 'high-resolution human proteins'?

Absolutely. The skill allows you to combine AttributeQueries using logical operators to filter results by organism, resolution, experimental method, and more.

What file formats are supported for structure downloads?

It supports the legacy PDB format, the modern mmCIF (PDBx) standard, and BinaryCIF for efficient data access.

Does it include AlphaFold models?

Yes, the RCSB PDB includes computed structure models like those from AlphaFold and ModelArchive, which can be accessed using specific ID prefixes.

PDB Database Explorer

Name: PDB Database Explorer
Author: jimmc414

byjimmc414

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324

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데이터 과학 및 ML

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

This skill enables Claude to interact directly with the RCSB Protein Data Bank (PDB), the global repository for biological macromolecular structures. It allows for sophisticated searching by text, amino acid sequence, or structural similarity across over 200,000 entries. Users can retrieve detailed metadata, download coordinates in PDB or mmCIF formats, and perform batch operations, making it an essential tool for bioinformaticians, medicinal chemists, and researchers working on protein engineering or autonomous scientific discovery.

주요 기능

01Multi-modal searching by text, sequence, and 3D structural similarity

02Batch processing support for large-scale structural analysis

03324 GitHub stars

04Direct coordinate download in PDB, mmCIF, and BinaryCIF formats

05Integration with BioPython for automated structure parsing and modeling

06Comprehensive metadata retrieval via GraphQL and Search APIs

사용 사례

01Identifying drug targets and analyzing ligand binding sites for pharmaceutical research

02Finding homologous structures to assist in protein folding and modeling tasks

03Automating the collection of high-resolution structural datasets for machine learning training

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add jimmc414/kosmos pdb-database

For use in Claude.ai and ChatGPT

Download Skill