Structural Bioinformatics
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Date:
Monday 3 - Friday 7 September 2018Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Tuesday 03 April 2018Application deadline:
Friday 08 June 2018Participation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
£540Registration closed
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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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 | |
