Course at EMBL-EBI

Structural bioinformatics

Welcome to the new EMBL-EBI Training site. Please tell us what you think!

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. Bioinformatics data derived from structure determination experiments enables life-science researchers to address a wide variety of questions. For example, it aids the understanding of how mutations in a gene might alter a protein’s shape, disrupt a catalytic site, or alter the binding affinity of a pharmaceutical compound.

This course explores bioinformatics data resources and tools for the interpretation and exploitation of biomacromolecular structures. It will focus on how best to analyse available structural data to gain useful information given specific research contexts. The course content will investigate the impact of genetic variation on structure, predicting protein structure and function, and exploring interactions with other macromolecules as well as with low-MW compounds. Participants will also have an opportunity to explore protein docking using HADDOCK.

Who is this course for?

This course is for biological researchers who want to learn more about the application of structural information in their work and how to use some of the key bioinformatics resources that are available. No previous experience in the field of structural bioinformatics is required, however a basic knowledge of protein structure would be of benefit. Participants should be familiar with basic Linux operations - - and have some experience of bioinformatics tools and databases.

What will I learn?

Learning outcomes

At the end of this course, trainees will be able to:

  • Access and browse a range of structural data repositories
  • Determine whether appropriate structural information exists about a given molecule or complex, applying available structure-quality information
  • Build a structural model for a protein which has a structurally characterised relative and evaluate its quality
  • Evaluate the potential impact of genetic variation on a structure
  • Predict the function of a protein based on sequence and structure data
  • Explore protein complex modelling approaches


Ajay Mishra
Gerard Kleywegt
Christine Orengo
University College London, UK
David Armstrong
Deepti Gupta
Rob Finn
Lorna Richardson
Franca Fraternali
Kings College London, UK
Osman Salih
Alexandre Bonvin
Utrecht University, Netherlands
Lawrence Kelley
Imperial College London
Anna Gaulton
Andrew Martin
University College London, UK
James Stephenson
Madan Babu
MRC Laboratory of Molecular Biology
Rodrigo Vargas Honorato
Utrecht University, Netherlands
Ian Sillitoe
University College London
Sjors Scheres
MRC Laboratory of Molecular Biology, Cambridge, UK


Day 1 – Monday 16th September 2019
12:00 – 13:00 Arrival, registration and lunch  
13:00 – 14:00 Welcome and introductions Ajay Mishra
14:00 – 14:30 Introduction to structural biology data Gerard Kleywegt
14:30 – 15:30 Introduction to PDBe resources & group activity David Armstrong / PDBe Team
15:30 – 16:00 Break  
16:00 – 17:30 Finding and validating structural data Deepti Gupta / PDBe Team
17:30 – 19:00 Poster session & drinks reception  
19:30 Dinner at Hinxton Hall  
Day 2 – Tuesday 17th September 2019
9:00 – 10:30 Fast, sensitive homology detection using HMMER Rob Finn
10:30 – 11:00 Break  
11:00 – 12:30 Sequence and structure based signatures Lorna Richardson
12:30 – 13:30 Lunch & posters  
13:30 – 15:00 Protein folds and structural family resources Ian Sillitoe
15:00 – 15:30 Break  
15:30 – 17:30 Protein structure prediction Lawrence Kelley
17:30 – 18:30 Keynote: Data driven approaches to biological systems Madan Babu
18:30 End of day  
19:30 Dinner at Hinxton Hall  
Day 3 – Wednesday 18th September 2019
9:00 – 11:00 Exploring protein docking with HADDOCK (lecture) Alexandre Bonvin
11:00 – 11:30 Break  
11:30 – 12:30 Exploring protein docking with HADDOCK (practical) Alexandre Bonvin / Rodrigo Vargas-Honorato
12:30 – 13:30 Lunch & posters  
13:30 – 14:30 Exploring protein docking with HADDOCK (practical cont.) Alexandre Bonvin / Rodrigo Vargas-Honorato
14:30 – 15:30 PDBe tools - how to analyse a structure David Armstrong / PDBe Team
15:30 – 16:00 Break  
16:00 – 18:00 PDBe-KB aggregated views of protein structure data David Armstrong / PDBe Team
18:00 End of day  
19:00 Dinner at Hinxton Hall  
Day 4 – Thursday 19th September 2019
9:00 – 11:00 Variant / mutation mapping James Stephenson
11:00 – 11:30 Break  
11:30 – 13:00 SAAPdb and other resources exploiting structure to determine the impacts of mutations Andrew Martin
13:00 – 14:00 Lunch & posters  
14:00 – 16:00 Resources for protein interactions and complexes Franca Fraternali
16:00 – 16:30 Break  
16:30 – 18:30 EM data and protein complexes Osman Salih
18:30 End of day  
19:30 Dinner at Red Lion, Hinxton  
Day 5 – Friday 20th September 2019
9:00 – 10:30 Drug discovery and ChEMBL Anna Gaulton and ChEMBL Team
10:30 – 11:00 Break  
11:00 – 12:00 Keynote: The Cryo-EM resolution revolution Sjors Scheres
12:00 – 13:00 Course discussion, wrap-up and feedback  
13:00 – 13:45 Lunch  
13:45 Shuttle to Cambridge Station (Stop 5)  

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

  1. Complete the online application form.
  2. Provide a Microsoft Word (.docx) document containing three short paragraphs with a biography, work history and description of your current research interests; each paragraph should be no more than 100 words.
  3. Provide a letter of support from a supervisor or a senior co-worker explaining why you should be selected for this course.

Please submit all documents to Marina Pujol ( by 12:00 GMT on Friday 14 June, 2019.

Incomplete applications will not be considered.

All participants are expected to present a poster that will be displayed during the course outside the training room. Please send your poster in PDF format to Marina Pujol ( and we will print it on campus. 

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.

Accommodation will be provided onsite at the Wellcome Genome Campus Conference Centre. Please contact them directly if you wish to arrange to stay additional nights around the course dates.

The course includes evening meals at the Hinxton Hall Restaurant on campus or the Red Lion Pub in nearby Hinxton village, and breaks and lunches outside the EMBL-EBI training rooms.

This course has ended

16 - 20 September 2019
European Bioinformatics Institute United Kingdom
Marina Pujol

  • Sarah Morgan
  • Christine Orengo
    University College London, UK
  • Gerard Kleywegt
  • Ajay Mishra

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