From sequences to structures: protein characterisation using EMBL-EBI APIs

Proteins are fundamental to biological processes, and understanding their sequence, structure, and function is crucial for various applications in research. 

This one-day, hands-on virtual workshop will guide you through a structured, programmatic workflow using EMBL-EBI resources. Learn how to retrieve protein sequences, identify homologs, annotate functional domains, and explore structural information using REST APIs. 

The course emphasises programmatic access (APIs) to integrate sequence, functional, and structural data into a unified analysis pipeline. Through a step-by-step Python workflow, you will apply different EMBL-EBI tools to analyse an example protein, gaining practical experience in automating large-scale protein data analysis.

Virtual course

This course will take place on Zoom. Trainers will be available to assist during practical sessions, answer questions, and provide further explanations during the Zoom.

To join the course, you will need to create an EMBL-EBI Training website account.

Who is this course for?

This course is designed for bioinformaticians and computational biologists who wish to learn how to automate the retrieval and analysis of protein-related data from EMBL-EBI resources for protein characterisation. 

It is recommended that you have a basic understanding of programming, ideally in Python, as the examples provided will be in Python.

What will I learn?

Learning outcomes

After completing the course, you will be able to:

• Describe various protein resources available at EMBL-EBI
• Understand the programmatic usage of EBI services for protein search
• Know how to integrate multiple EMBL-EBI tools for comprehensive data analysis
• Gain practical experience through guided hands-on activities

Course content

During the course, you will learn how to use EMBL-EBI APIs to: 

• Retrieve protein sequences and metadata from UniProt and run sequence analysis
• Detect functional domains of proteins using InterPro
• Search for entries for experimentally solved protein structures in PDBe and annotate functional sites using PDBe-KB
• Retrieve AlphaFoldDB models for AI-predicted protein structures

Trainers

Places will be allocated on a first-come first-served basis, so please register soon to avoid disappointment. Incomplete registrations will not be processed.