Which file formats can I download for 3D structures?

The skill supports downloading coordinates in several formats, including the modern mmCIF standard, the legacy PDB text format, and efficient BinaryCIF files.

Does this skill support AlphaFold models?

Yes, the RCSB PDB index includes computed structure models like those from AlphaFold, which can be retrieved using 'AF_' prefixes.

What is the RCSB PDB?

The RCSB Protein Data Bank (PDB) is the global repository for 3D structural data of biological macromolecules, containing hundreds of thousands of protein and nucleic acid structures.

How do I install the necessary dependencies for this skill?

You can install the primary API client by running 'uv pip install rcsb-api' in your terminal.

Can I search for structures by protein sequence?

Yes, this skill supports sequence similarity searches to find PDB entries that match a specific amino acid or nucleotide sequence using E-value and identity cutoffs.

PDB Database Access

Name: PDB Database Access
Author: x-cmd

byx-cmd

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データサイエンスとML

Accesses the RCSB Protein Data Bank to search, retrieve, and analyze 3D structural data for biological macromolecules.

概要

This skill enables Claude to interact directly with the RCSB Protein Data Bank (PDB), the worldwide repository for 3D structural data of proteins and nucleic acids. It provides programmatic capabilities to search over 200,000 experimentally determined structures and computed models using text queries, sequence similarity, or structural geometry. By facilitating the download of coordinates in PDB or mmCIF formats and the retrieval of detailed experimental metadata, this skill is essential for researchers and developers working in drug discovery, protein engineering, and computational structural biology who wish to automate their data gathering and analysis workflows within an AI-enhanced environment.

主な機能

8 GitHub stars
Coordinate downloading in PDB, mmCIF, and BinaryCIF formats
Flexible GraphQL support for custom structural data queries
Batch processing patterns for efficient multi-structure data retrieval
Multi-criteria search including text, attribute, sequence, and structure similarity
Metadata retrieval for experimental methods, resolution, and quality metrics

ユースケース

Creating curated structural datasets for training machine learning models in biology
Automating drug target identification and ligand binding site analysis for pharmacology
Retrieving homologous structures and sequences for protein design and modeling

概要

主な機能

8 GitHub stars
Coordinate downloading in PDB, mmCIF, and BinaryCIF formats
Flexible GraphQL support for custom structural data queries
Batch processing patterns for efficient multi-structure data retrieval
Multi-criteria search including text, attribute, sequence, and structure similarity
Metadata retrieval for experimental methods, resolution, and quality metrics

ユースケース

Creating curated structural datasets for training machine learning models in biology
Automating drug target identification and ligand binding site analysis for pharmacology
Retrieving homologous structures and sequences for protein design and modeling