Does this skill provide access to AlphaFold models?

Yes, it can access computed structure models (CSMs) from AlphaFold and ModelArchive using their respective prefixes within the RCSB ecosystem.

What structural file formats can I download with this skill?

You can download coordinate files in PDB (legacy), mmCIF (modern standard), and BinaryCIF formats, as well as specific biological assemblies.

Is it possible to query metadata like resolution or experimental method?

Absolutely. You can perform attribute searches to filter structures by resolution, experimental method (X-ray, Cryo-EM, etc.), deposition date, and more.

Can I search for proteins using only a fasta sequence?

Yes, the skill supports Sequence Similarity searches where you can define identity thresholds and E-value cutoffs to find matching structures.

How does the skill handle multiple structures at once?

The skill is designed for batch operations, allowing you to iterate through lists of PDB IDs to fetch metadata or download files programmatically.

RCSB PDB Structure Access

Name: RCSB PDB Structure Access
Author: pur3v4d3r

bypur3v4d3r

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데이터 과학 및 ML

Enables seamless programmatic access to the RCSB Protein Data Bank for searching, retrieving, and analyzing 3D molecular structures.

The PDB Database skill empowers Claude to interact directly with the RCSB Protein Data Bank (PDB), the global repository for 3D structural data of biological macromolecules. It provides comprehensive tools for searching structures by text, sequence, or geometry, and enables the direct download of coordinate files in PDB and mmCIF formats. This skill is essential for bioinformatics workflows, drug discovery research, and protein engineering, allowing users to automate data retrieval, perform batch operations, and integrate structural metadata into computational pipelines with ease.

주요 기능

01Direct coordinate downloads for PDB, mmCIF, and BinaryCIF file formats

021 GitHub stars

03Advanced search capabilities including text, attribute, sequence, and structure similarity

04Access to comprehensive experimental metadata, quality metrics, and biological assemblies

05Flexible data retrieval using optimized REST and GraphQL API queries

06Batch operation support for efficient processing of multiple structure entries

사용 사례

01Building automated bioinformatics pipelines for structural biology and sequence-structure research

02Identifying and downloading homologous structures for protein modeling and engineering

03Automating drug target structure retrieval and binding site analysis for virtual screening

What are Skills?·How to Install

Install with 🐟 Skill.Fish

npx skillfish add pur3v4d3r/pur3-pkb-codebase pdb-database

For use in Claude.ai and ChatGPT

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