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.

Successful participants may be sent materials prior to the course. These might include pre-recorded talks and required reading or online training that will be essential to fully engage with the course.

Who is this course for?

This course is aimed at scientists generating structural data or scientists utilising structural data in their 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 (PDB) and Electron Microscopy Data Bank (EMDB), and tools to search and analyse information in these repositories from Protein Data Bank in Europe (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
• Tools and resources for drug discovery: ChEMBL
• AI-predicted protein structures: AlphaFoldDB and AlphaFill

Trainers

Please read our page on application support before starting your application. In order 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 18 June 2023. Items marked * in the application are mandatory. Incomplete registrations will not be processed. 

All applicants will be informed of the status of their application (successful, waiting list, unsuccessful) by 3 July 2023. If you have any questions regarding the application process please contact Sophie Spencer. 

The registration fee of £825.00 includes:

• Catering as detailed on the course programme
• Accommodation for four nights (2, 3, 4, and 5 October)
• Bespoke course handbook with links to all course materials
• Use of a computer in the EMBL-EBI training suite throughout the course
• Shuttle bus on the final course day to Cambridge train station 

Accommodation 

Hotel rooms will be provided onsite at Hinxton Hall Conference Centre. Please contact them directly if you wish to arrange to stay additional nights around the course dates.

Catering

The course includes catering as detailed on the programme tab. Successful applicants will be asked for any dietary requirements and allergies upon registration. 

Posters

All participants are expected to present a poster that will be displayed during the course outside the training room. Successful applicants will be asked to submit their posters upon registration. We will print these for you and have them available when you arrive on-site.

All posters should:

•         be A2 in size – 420mm x 594 mm
•         be in a portrait orientation
•         include your photograph and contact information

We expect the posters to act as a talking point between you, other participants and the trainers on the course. The posters will be displayed throughout the week so people can view them during breaks and lunch. 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 gathered participants.