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

Data Science & ML

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

About

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.

Key Features

Multi-modal searching by text, sequence, and 3D structural similarity
Batch processing support for large-scale structural analysis
324 GitHub stars
Direct coordinate download in PDB, mmCIF, and BinaryCIF formats
Integration with BioPython for automated structure parsing and modeling
Comprehensive metadata retrieval via GraphQL and Search APIs

Use Cases

Identifying drug targets and analyzing ligand binding sites for pharmaceutical research
Finding homologous structures to assist in protein folding and modeling tasks
Automating the collection of high-resolution structural datasets for machine learning training

About

Key Features

Multi-modal searching by text, sequence, and 3D structural similarity
Batch processing support for large-scale structural analysis
324 GitHub stars
Direct coordinate download in PDB, mmCIF, and BinaryCIF formats
Integration with BioPython for automated structure parsing and modeling
Comprehensive metadata retrieval via GraphQL and Search APIs

Use Cases

Identifying drug targets and analyzing ligand binding sites for pharmaceutical research
Finding homologous structures to assist in protein folding and modeling tasks
Automating the collection of high-resolution structural datasets for machine learning training