Structural Bioinformatics 2016

Date:

 Tuesday 20 Friday 23 September 2016

Venue: 

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

Application opens: 

Thursday May 05 2016

Application deadline: 

Friday July 29 2016

Participation: 

Open application with selection

Contact: 

Johanna Langrish

Registration fee: 

£600

Registration closed

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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