Structural Bioinformatics

Date:

 Monday 3 Friday 7 September 2018

Venue: 

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

Application opens: 

Tuesday April 03 2018

Application deadline: 

Friday June 08 2018

Participation: 

Open application with selection

Registration fee: 

£540

Registration closed

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Overview

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.

 If you would like to see details of similar course from previous years, please take a look at our course listings, using the filter boxes to refine your search by year and subject.

Audience

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 - http://www.ee.surrey.ac.uk/Teaching/Unix/ - and have some experience of bioinformatics tools and databases.

Outcomes

  • 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 

Programme

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 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 Christine Orengo 
15:00-15:30 Break  
15:30-17:00 Function prediction practical 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  
14:00-15:30 Exploring protein docking with HADDOCK Alexandre Bonvin
15:30-16:00 Break  
16:00-17:00 Exploring protein docking with HADDOCK Alexandre Bonvin
17:00-18:00 Structural bioinformatics - past and future + Discussion Janet Thornton
18:00 End of day  
19:30 Evening meal at Red Lion, Hinxton  

Day 4 – Thursday 6 September 2018

08:45 Arrival  
09:00-11:00 SAAPdb and other resources exploiting structure to determine the impacts of mutations Andrew Martin 
11:00-11:30 Break  
11:30-13:00 Ensembl: Variant Effect Predictor Ensembl Team
13:00-14:00 Lunch and posters  
14:00-16:00 TBC TBC 
16:00-16:30 Break  
16:30-18:30 PDBe tools – how to analyse a structure (Seq to Struct, Ligands, API) David Armstrong / PDBe Team
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 Ardan Patwardhan  / EMDB Team
10:00-11:15 Drug discovery and ChEMBL Anna Gaulton / ChEMBL + ChEBI Team
11:15-11:45 Break  
11:45-13:00 Keynote lecture TBC 
13:00-13:15 Course discussion and feedback Piv Gopalasingam
13:15-13:45 Lunch  
13:45 Coach to Cambridge Railway Station