Structural Bioinformatics
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Date:
Monday 12 - Friday 16 October 2015Venue:
European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Monday 15 June 2015Application deadline:
Friday 07 August 2015Participation:
Open application with selectionContact:
Frank O’DonnellRegistration fee:
£695Registration closed
Overview
This course will explore bioinformatics data resources and tools that are available for the interpretation and exploitation of biomacromolecular structures, focusing on how best to use structural information to gain the most from it in specific research contexts. This will include investigating the impact of genetics variation on structure, predicting protein structure and function and exploring interactions with other macromolecules as well as with low-MW compounds.
Audience
This course is aimed at researchers who want to learn more about the application of structural information in their work and how to use the bioinformatics resources that are available. No previous experience of structural bioinformatics is required.
Syllabus, tools and resources
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 PDBe (Protein Data Bank in Europe)
- Computational approaches to structure prediction: ModBase, Rosetta, PHYRE, Interactome 3D
- Impact of genetic variation on protein structure: Ensembl VEP, DBSeq, SAAPdb
- Protein analysis and classification: Pfam, CATH, SCOP, InterPro, PDBeFold, PDBePISA, ProFunc
- Tools and resources for drug discovery: ChEMBL
Outcomes
After this course you should be able to:
- Access and browse structural data repositories to determine whether appropriate structural information exists, including the use of structure-quality information
- Build a structural model for a protein having a structurally characterised relative and evaluate its quality.
- Evaluate the potential impact of genetic variation on a structure
- Determine the potential function of a protein based on sequence and structure dataH
Programme
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - Monday 12 October | ||
| Bringing structure to biology | ||
| 11:30 | Arrival at Wellcome Genome Campus and course registration | |
| 12:00 | Lunch | |
| 12:30 | Welcome and introductions | Tom Hancocks |
| 13:00 | Introduction to structural biology data | Gerard Kleywegt |
| 13:30 | Practical
|
Sanchayita Sen & David Armstrong |
| 15:00 | Break | |
| 15:30 | Practical
|
Sanchayita Sen & David Armstrong |
| 16:30 | Molecular graphics tools | Sanchayita Sen & David Armstrong |
| 18:00 | End of day | |
| 18:15 | Evening meal at Hinxton Hall | |
| 20:00 | Coach to Whittlesford Holiday Inn | |
| Day 2 - Tuesday 13 October | ||
| New structures from old | ||
| 08:30 | Coach to Wellcome Genome Campus | |
| 09:00 | Protein structure prediction | Lawrence Kelley & Michael Sternberg |
| 11:00 | Break | |
| 11:30 | Modelling trans-membrane proteins | David Jones |
| 12:30 | Lunch | |
| 13:30 | Resources for protein interactions and complexes | Franca Fraternali |
| 15:00 | Tea/coffee break | |
| 15:30 | Resources for protein interactions and complexes | Franca Fraternali |
| Genetic variation and protein structure | ||
| 16:30 | The impact of genetic mutations - Ensembl: Variation Effect Predictor | Will McClaren, Sarah Hunt |
| 18:30 | End of day | |
| 19:00 | Evening meal at Red Lion pub, Hinxton | |
| 21:30 | Coach to Whittlesford Holiday Inn | |
| Day 3 - Wednesday 14 October | ||
| Genetic variation and protein structure | ||
| 08:30 | Coach to Wellcome Genome Campus | |
| 09:00 | SAAPdb and other resources exploiting structure to determine the impacts of mutations | Andrew Martin |
| 11:00 | Break | |
| 11:30 | Keynote lecture | Tom Blundell |
| 12:30 | Lunch | |
| 13:30 | Methods predicting the impact of genetic variations | Michael Sternberg |
| 14:30 | Methods predicting the impact of genetic variations | Julian Gough |
| 15:30 | Break | |
| 16:00 | Cancer mutations | Franca Fraternali |
| 17:30 | End of day | |
| 18:15 | Evening meal at Hinxton Hall | |
| 20:00 | Coach to Whittlesford Holiday Inn | |
| Day 4 - Thursday 15 October | ||
| From structure to function | ||
| 08:30 | Coach to Wellcome Genome Campus | |
| 09:00 | Protein folds and structural family resources | Christine Orengo |
| 11:00 | Break | |
| 11:30 | Fast, sensitive homology detection using HMMER | Rob Finn |
| 13:00 | Lunch | |
| 14:00 | Sequence and structure-based signatures | Alex Mitchell |
| 15:30 | Break | |
| 16:00 | Function prediction practical | Roman Laskowski |
| 18:00 | End of day | |
| 18:15 | Dinner at Hinxton Hall | |
| 20:00 | Coach to Whittlesford Holiday Inn | |
| Day 5 - Friday 16 October | ||
| Small molecules with big effects | ||
| 08:30 | Coach to Wellcome Genome Campus | |
| 09:00 | Drug discovery and ChEMBL | ChEMBL Team |
| 11:00 | Special lecture: Evolution & Assembly of Protein Complexes | Sarah Teichmann |
| 12:00 | Lunch | |
| 13:00 | Group projects | All |
| 15:00 | Project presentation | All |
| 16:00 | Course discussion and feedback | Tom Hancocks |
| 16:20 | End of course | |
| 16:30 | Coach to Cambridge Train Station | |