Structural Bioinformatics 2016
The application system requires cookies, and the limited processing of your personal data in order to function. By applying to this course you are agreeing to this as outlined in our Privacy Notice and Terms of Use
Date:
Tuesday 20 - Friday 23 September 2016Venue:
European Bioinformatics Institute (EMBL-EBI) - Training Room 1 - Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, United KingdomApplication opens:
Thursday 05 May 2016Application deadline:
Friday 29 July 2016Participation:
Open application with selectionContact:
Johanna LangrishRegistration fee:
£600Registration closed
Overview
- This course will explore bioinformatics data resources and tools 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 genetic 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 wanting 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 work in the field of structural bioinformatics is required. Participants should be familiar with basic Linux operations and have experience of basic bioinformatics tools and databases.
Syllabus, tools and resources
- 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: 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
- Predict the function of a protein based on sequence and structure data
- Located additional small molecule data for your structure of interest
Programme
| Time | Topic | Trainer |
|---|---|---|
| Day 1 - Tuesday 20 September 2016 | ||
| 12:00 - 13:00 | Arrival, registration and lunch | |
| 13:00 - 14:00 | Welcome and introductions | Tom Hancocks |
| 14:00 - 14:30 | Introduction to structural biology data | Gerard Kleywegt |
| 14:30 - 15:30 | Structural bioinformatics practical | PDBe Team |
| 15:30 - 16:00 | Break | |
| 16:00 - 18:00 | Structural bioinformatics practical | PDBe Team |
| 18:00 - 18:30 | Discussion session | All |
| 18:30 | End of day | |
| 19:00 |
Evening meal at Hinxton Hall - (Green Room) |
|
| 20:30 |
Coach to Whittlesford Holiday Inn |
|
| Day 2 - Wednesday 21 September 2016 | ||
| 08:45 | Coach to Wellcome Genome Campus | |
| 09:00 - 11:00 | Resources for protein interactions and complexes | Franca Fraternali |
| 11:00 - 11:15 | Break | |
| 11:15 - 13:15 | Protein structure prediction | Lawrence Kelley |
| 13:15 - 14:00 | Lunch and posters | |
| 14:00 - 15:30 | Fast, sensitive homology detection using HMMER | Rob Finn |
| 15:30 - 16:00 | Break | |
| 16:00 - 18:00 | Sequence and structure-based signatures | Alex Mitchell |
| 18:00 | End of day | |
| 18:30 | Evening meal at - The Red Lion Pub, Hinxton | |
| 20:30 | Coach to Whittlesford Holiday Inn | |
| Day 3 - Thursday 22 September 2016 | ||
| 08:45 | Coach to Wellcome Genome Campus | |
| 09:00 - 10:30 | Ensembl: Variant Effect Predictor | Will McClaren |
| 10:30 - 11:00 | Break | |
| 11:00 - 13:00 | Protein folds and structural family resources |
Christine Orengo |
| 13:00 - 14:00 | Lunch and posters | |
| 14:00 - 15:00 | Keynote | Janet Thornton |
| 15:00 - 15:30 | Discussion session | |
| 15:30 - 16:00 | Break | |
| 16:00 - 18:00 | Resources exploiting structure to determine the impacts of mutations | Andrew Martin |
| 18:00 | End of day | |
| 18:30 | Evening meal at Hinxton Hall - (Restaurant) | |
| 20:00 | Coach to Whittlesford Holiday Inn | |
| Day 4 - Friday 23 September 2016 | ||
| 08:45 | Check-out and coach to Wellcome Genome Campus | |
| 09:00 - 10:30 | Drug discovery and ChEMBL | Prudence Mutowo |
| 10:30 - 11:00 | Break | |
| 11:00 - 13:00 | Function prediction practical | Roman Laskowski |
| 13:00 - 13:15 |
Course discussion and feedback |
|
| 13:15 - 14:00 | Lunch | |
| 14:15 | Coach to Cambridge Railway Station | |
Please note: This programme is subject to minor changes prior to the course, but the start and end times will remain fixed