Is AlphaFold DB data free to use for research?

Yes, AlphaFold DB data is provided by DeepMind and EMBL-EBI under a Creative Commons Attribution 4.0 International (CC BY 4.0) license.

What Python libraries are required for the AlphaFold skill?

For full functionality, it is recommended to install Biopython, requests, and optionally the Google Cloud BigQuery and gsutil packages for bulk data access.

How do I retrieve a protein structure using this skill?

You can use the provided Biopython patterns or direct REST API calls to query the AlphaFold DB by UniProt accession ID and download mmCIF or PDB coordinate files.

What are pLDDT and PAE metrics in AlphaFold?

pLDDT measures per-residue local confidence (0-100), while PAE (Predicted Aligned Error) indicates the confidence level in the relative positioning of different protein domains.

AlphaFold Database Access

Name: AlphaFold Database Access
Author: pur3v4d3r

bypur3v4d3r

•

数据科学与机器学习

Accesses and analyzes over 200 million AI-predicted protein structures for drug discovery and structural biology research.

This skill integrates AlphaFold DB's massive repository of AI-predicted 3D protein structures directly into computational workflows. It enables developers and researchers to retrieve protein structures using UniProt IDs, download coordinate files in PDB or mmCIF formats, and interpret critical confidence metrics like pLDDT and PAE. Whether performing single-protein analysis or large-scale proteome studies via Google Cloud, this skill provides the implementation patterns needed to bridge the gap between AI-driven structural predictions and practical biological research applications.

主要功能

01Integrate structural data into Biopython and bioinformatics pipelines

02Analyze prediction reliability using pLDDT and PAE confidence metrics

03Download model coordinates in high-fidelity mmCIF and PDB formats

041 GitHub stars

05Access bulk proteome datasets via Google Cloud Storage and BigQuery

06Retrieve 3D protein structures via UniProt IDs and protein names

使用场景

01Large-scale structural proteomics and proteome-wide data analysis

02Protein engineering and mutation modeling in high-confidence regions

03Structure-based drug discovery and target protein docking studies

What are Skills?·How to Install

Install with 🐟 Skill.Fish

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

For use in Claude.ai and ChatGPT

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