Structural Bioinformatics


 Monday 3 Friday 7 September 2018


European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus Hinxton,  Cambridge CB10 1SD,  United Kingdom

Application opens: 

Tuesday 03 April 2018

Application deadline: 

Friday 08 June 2018


Open application with selection


Frank O’Donnell

Registration fee: 


Registration closed

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Structural biology, determining the three-dimensional shape of a protein, can tell us a lot about how a protein functions and the role it plays within a cell. Bioinformatics data derived from structural determination experiments can aid biological researchers asking a wide variety of questions. It aides the understanding of how DNA mutations 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 bio-macromolecular 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.

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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. Participants should be familiar with basic Linux operations - - and have some experience of bioinformatics tools and databases.


  • Access and browse a range of structural data repositories
  • Determine whether appropriate structural information exists, 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 


Day 1 – Monday 3 September 2018

12:00-13:00 Arrival, registration and lunch  
13:00-14:00 Welcome and introductions Piv Gopalasingam
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  
16:00-18:30 Finding and validating structural data Deepti Gupta / David Armstrong / PDBe Team
18:30 End of day  
19:30 Dinner at Hinxton Hall  

Day 2 – Tuesday 4 September 2018

08:45 Arrival  
09:00-10:30 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 and posters  
13:30-15:00 Protein folds and structural family resources Ian Sillitoe 
15:00-15:30 Break  
15:30-17:00 Protein structure and disease-associated variants Roman Laskowski 
17:00-18:30 PDBe tools – how to analyse a structure (PISA + FOLD)  David Armstrong / PDBe Team 
18:30 End of day  
19:30 Dinner at Hinxton Hall  

Day 3 – Wednesday 5 September 2018

08:45 Arrival  
09:00-11:00 Protein structure prediction Lawrence Kelley 
11:00-11:30 Break  
11:30-13:00 Exploring protein docking with HADDOCK Alexandre Bonvin
13:00-14:00 Lunch and posters  
14:00-16:15 Exploring protein docking with HADDOCK Alexandre Bonvin
16:15-16:45 Break  
16:45-17:45 Structural bioinformatics - past and future + Discussion Janet Thornton
17:45 End of day  
19:30 Dinner at Hinxton Hall  

Day 4 – Thursday 6 September 2018

08:45 Arrival  
09:00-11:00 PDBe tools – how to analyse a structure (Seq to Struct, Ligands, API) David Armstrong / PDBe Team
11:00-11:30 Break  
11:30-13:00 Ensembl: Variant Effect Predictor Emily Perry
13:00-14:00 Lunch and posters  
14:00-16:00 Resources for protein interactions and complexes Anna Laddach 
16:00-16:30 Break  
16:30-18:30 SAAPdb and other resources exploiting structure to determine the impacts of mutations Andrew Martin 
18:30 End of day  
19:30 Dinner at Hinxton Hall  

Day 5 – Friday 7 September 2018

08:45 Check out and arrival  
09:00-10:00 EM data and protein complexes Osman Salih
10:00-11:15 Drug discovery and ChEMBL Anna Gaulton / ChEMBL + ChEBI Team
11:15-11:45 Break  
11:45-12:45 Keynote lecture Sarah Teichmann 
12:45-13:15 Course discussion and feedback Piv Gopalasingam
13:15-13:45 Lunch  
13:45 Coach to Cambridge Railway Station