Structural bioinformatics

This course provides a guide to the commonly used methods and tools in structural bioinformatics to analyse and interpret experimentally determined and AI-predicted macromolecular structure data.

Structural biology, determining the three-dimensional shapes of biomacromolecules and their complexes, can tell us a lot about how these molecules function and the roles they play within a cell. Data derived from structure determination experiments and Artificial Intelligence (AI)-assisted structure prediction enables life-science researchers to address a wide variety of questions.  

This course explores bioinformatics data resources and tools for the investigation, analysis, and interpretation of both experimentally determined and predicted biomacromolecular structures. It will focus on how best to analyse and interpret available structural data to gain useful information given specific research contexts. The course content will also cover predicting function and exploring interactions with other macromolecules.

Virtual course

You will learn via a mix of pre-recorded lectures, live presentations, and trainer Q&A sessions. Practical experience will be developed through group activities and trainer-led computational exercises. Live sessions will be delivered using Zoom with additional support and asynchronous communication via Slack.

Pre-recorded material may be provided before the course starts that you will need to watch, read, or work through to gain the most out of the actual training event. A brief pre-course session will be held the week beforehand. Computational practicals will run on EMBL-EBI's virtual training infrastructure, meaning you will not require access to a powerful computer or install complex software on your own machines.

You will need to be available between the hours of 09:00 – 18:30 BST each day of the course. Trainers will be available to assist, answer questions, and provide further explanations during these times.

Who is this course for?

This course is aimed at you if you are a scientist generating structural data or a scientist utilising structural data in your analysis and/or interpretation. No previous experience in the field of structural bioinformatics is required, however good knowledge of protein structure and function would be of benefit.

What will I learn?

Learning outcomes

After the course, you should be able to:

• Access and browse a range of structural data repositories
• Determine whether appropriate structural information exists about a given small molecule, macromolecule or complex, applying available structure-quality information
• Build a structural model for a protein which has a structurally characterised relative and evaluate its quality
• Predict the function of a protein, based on sequence and structure data, and navigate and assess AI-predicted protein structures
• Explore protein-complex modelling approaches

Course content

During this course, you will learn about: 

• Public repositories of structural data: Protein Data Bank (PDBe) and Electron Microscopy Data Bank (EMDB), and tools to search and analyse information in these repositories from PDBe, including PDBe-KB.
• UniProt and basic Sequence alignment tools
• Protein structure analysis and classification: HMMER, InterPro, CATH
• Protein structure prediction and docking: PHYRE2 and HADDOCK
• Structure validation and assessment tools and strategies: PDB-REDO
• Tools and resources for drug discovery: ChEMBL

AI-predicted protein structures: AlphaFoldDB and AlphaFill

Trainers

Please read our support page before starting your application. To be considered for a place on this course, you must do the following:

• Complete the online application form.
• Ensure you add relevant information to the ‘submission details’ section where you are asked to provide information on your:
  • pre-requisite skills and knowledge
  • current work and course expectations
  • data availability
  • Upload one letter of support from your supervisor or a senior colleague detailing reasons why you should be selected for the course.

Please submit all documents during the application process by 23:59  BST on 19 July 2026. Items marked * in the application are mandatory. Incomplete applications will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 3 August 2026.  If you have any questions regarding the application process, please contact Sophie Spencer.

Posters
If selected for this course, you will be asked to submit your poster upon registration. We expect the posters to act as a talking point between you, other attendees, and the trainers on the course. They should give the reader an idea of the work you are engaged in, what you are planning to do next, and anything of interest that might be useful for sharing with the group.

Registration fees 

Payment must be completed within 14 days of receiving your acceptance email. Failure to do so may result in your place being offered to someone else on the waitlist.

Your registration fee includes: 

• access to the full five-day course programme
• access to a bespoke online course handbook
• secure community space on Slack
• virtual machine to work on that is accessed via the internet
• dedicated online support team
• certificate on completion of the course

We are grateful to UKRI for providing funding for this course. This has allowed us to offer a reduced course fee.

* If your company is an EMBL-EBI Industry Programme Member, discounts may be available. This will apply automatically on registration if applicable; alternatively, please contact your Event Organiser for more information.

Financial assistance
Financial assistance is available to a limited number of participants attending this course.

Registration fee waivers
A limited number of registration fee waivers are offered for this course.

• Application process:
  • Apply for the fee waiver alongside your course application.
  • Provide a brief explanation of why you require the waiver and how attending the course will benefit your career.
• Notification:
  • You will be informed of your waiver status at the same time as the outcome of your course application.
  • If awarded, the registration fee will be waived entirely.

Financial assistance terms and conditions

• Selection process: Recipients of financial assistance will be selected by the scientific organisers during the course application review.
• Selection criteria:
  • Selection is based on scientific merit, your current work or study location, the need for financial support, and the career impact of attending the course.
  • Priority will be given to applicants from Low- and Middle-Income Countries (LMICs).
• Fair consideration: Applying for financial assistance will not impact the outcome of your course application.

Event terms and conditions

• Selection process: Recipients will be selected by the scientific organisers during the course application review.
• Selection criteria:
  • Selection is based on scientific merit, your current work or study location, the need for financial support, and the career impact of attending the course.
  • Priority will be given to applicants from Low- and Middle-Income Countries (LMICs).
• Fair consideration: Applying for financial assistance will not affect your course application outcome.

Course materials

• The materials for the previous iterations are available for you to browse. These provide a snapshot of the content that will be covered in the 2026 course.