This repository contains Google Colab notebooks developed as part of the EMBL-EBI course "From sequences to structures: Protein characterisation using EMBL-EBI APIs 2025".
This collection of notebooks offers practical, hands-on tutorials for interacting with EMBL-EBI's powerful bioinformatics APIs. The primary focus is on the AlphaFold Database API, enabling researchers and students to programmatically access, retrieve, and utilise predicted protein structure data.
This notebook serves as the foundational introduction to the AlphaFold Database API. It covers:
- API Request Formulation: How to construct and send basic API requests to retrieve protein structure prediction data.
- Response Interpretation: Understanding the structure and content of the data returned by the API.
- Programmatic Downloads: Methods for downloading protein structure files (PDB, CIF) and associated data (such as Predicted Aligned Error (PAE) images and AlphaMissense annotations) directly to your Google Drive.
This notebook focuses on methods to visualise and interpret the data retrieved from the AlphaFold Database, specifically:
- Parsing pLDDT Scores: Extracting per-residue confidence metrics from protein structure files.
- Visualising pLDDT: Plotting confidence scores along the protein sequence to identify reliably predicted regions.
- Analysing PAE matrices: Creating visualisations of Predicted Aligned Error to assess the relative confidence of different parts of a protein structure.
- Plotting AlphaMissense data: Visualising variant effect predictions from AlphaMissense vs pLDDT.
This notebook provides a guide to accessing and querying AlphaFold Database information using Google BigQuery. Key topics include:
- BigQuery Setup: Instructions on setting up a BigQuery environment to interact with AlphaFold data.
- Basic Queries: Constructing SQL queries to retrieve specific protein metadata.
- Advanced Data Analysis: Performing complex queries for filtering, aggregating, and analysing AlphaFold data.
These materials are directly aligned with the learning objectives of the EMBL-EBI course: "From sequences to structures: Protein characterisation using EMBL-EBI APIs 2025". For more information about the course, please refer to the official EMBL-EBI Training website
To begin using these notebooks:
- Click the Open in Colab badge next to a notebook.
- In Colab, run the cells from top to bottom.
- Sign in to your Google account if needed, especially for saving files or mounting Google Drive.