Structural Bioinformatics

Date:

 Monday 23 Friday 27 October 2017

Venue: 

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

Application opens: 

Friday May 12 2017

Application deadline: 

Friday August 11 2017

Participation: 

Open application with selection

Contact: 

Emily Rees

Registration fee: 

£650

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.

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.

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: ModBase, Rosetta, PHYRE, Interactome 3D
  • Protein docking: HADDOCK
  • 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 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 

Additional information

All participants are expected to bring poster that will be displayed during the course outside the training room. Posters should include information on your current research interests and how the course relates to this work.

All posters should:

  • be A2 in size - 420mm x 594 mm
  • be in a portrait orientation
  • include your photograph and contact information

Catering is provided throughout the duration of the course.

All participants will be accommodated at the Wellcome Genome Campus Conference Centre for four nights.

Programme

Time Topic Trainer
Day 1 - Monday 23 October 2017
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

Introduction to PDBe resources & group activity

David Armstrong
15:30 - 16:00 Break  
16:00 - 18:30

Finding and validating structural data

David Armstrong
18:30 End of day   
19:30 Evening meal at Hinxton Hall Restaurant  
Day 2 - Tuesday 24 October 2017
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 - 17:30 Function prediction practical Roman Laskowski
17:30 - 18:30 Rare diseases and drug resistance Tom Blundell
18:30 End of day  
19:30 Evening meal at Hinxton Hall Restaurant  
Day 3 - Wednesday 25 October 2017
08:45 Arrival  
09:00 - 10:30

Exploring protein docking with HADDOCK

Alexandre Bonvin
10:30 - 11:00 Break  
11:00 - 12:30

Exploring protein docking with HADDOCK

Alexandre Bonvin

12:30 - 13:30 Lunch and posters  
13:30 - 14:30  Exploring protein docking with HADDOCK

Alexandre Bonvin

14:30 - 15:30 Structural bioinformatics - past and future

Janet Thornton

15:30 - 16:00

Discussion

 
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  
19:00 Evening meal at Hinxton Hall Restaurant   
Day 4 - Thursday 26 October 2017
08:45 Arrival  
09:00 - 10:30 Ensembl: Variant Effect Predictor Will Mclaren
10:30 - 11:00 Break  
11:00 - 13:00

Resources for protein interactions and complexes

Franca Fraternali
13:00 - 14:00 Lunch  
14:00 - 16:00

PDBe tools – how to analyse a structure

David Armstrong
16:00 - 16:30 Break  
16:30 - 17:30 PDBe tools – how to analyse a structure David Armstrong
17:30 - 18:30

EM data and protein complexes

Ardan Patwardhan
19:30 Evening meal at Red Lion Hinxton   
Day 5 - Friday 27 October 2017
08:45 Check-out and arrival  
09:00 - 11:00 Protein structure prediction Lawrence Kelley
11:00 - 11:30 Break  
11:30 - 13:00 Drug discovery and ChEMBL Prudence Mutowo 
13:00 - 13:15 Course feedback and wrap up Tom Hancocks 
13:15 - 13:45 Lunch  
13:45 Coach to Cambridge Station