Bioinformatics resources for protein biology

Date:

 Tuesday 26 Thursday 28 September 2017

Venue: 

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

Application opens: 

Monday June 05 2017

Application deadline: 

Friday September 08 2017

Participation: 

First come, first served

Contact: 

Frank O’Donnell

Registration fee: 

£120

Registration closed

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Overview

Are you aware of the wide range of protein data resources that can easily be accessed and explored to enhance your research? Do you want to know more about the sequence of your protein and its functions? Wondered whether a structure of your protein exists and how to explore it? Want to know more about the potential complexes and reaction pathways your protein of interest is involved in, giving you a better overview of its biological context?

This three day workshop will introduce you to data resources and tools developed by EMBL-EBI that can help you in your protein studies. Each day will focus on a particular protein topic, with the aim of helping you get more from your data and also to explore publically-available data that can further support your research.

Workshop topics

Day 1:(26th September): Where can I find protein sequence, classification and comparison information?

Day 2:(27th September): How do I choose a “good” protein structure and what can I learn from it?

Day 3:(28th September): What interactions, complexes and pathways is my protein involved in?

Audience

This workshop is aimed at anyone interested in finding out more about protein biology. No prior experience of bioinformatics is required, but an undergraduate level understanding of biology would be of benefit.

Syllabus, tools and resources

Day 1: UniProtKB, InterPro, HMMER

Day 2: PDBe search, PDBePISA and PDBeFOLD tools, EM DataBank

Day 3: IntAct, Complex Portal, Reactome

Outcomes

At the end of the workshop you should be able to:

  • Access and explore a range of appropriate protein resources
  • Use these resource to retrieve relevant protein information
  • Apply the information you have discovered in your research

Programme

Time Topic Trainer
Day 1 - Where can I find protein sequence, classification and comparison information?
9:00 - 9:15 Registration  
9:15 - 9:30 Welcome and Course introduction Sarah Morgan
9:30 - 11:00 UniProt Sangya Pundir
11:00 - 11:15 Tea/coffee break  
11:15 - 12:45 UniProt Klemens Pichler
12:45 - 13:30 Lunch  
13:30 - 15:15 HMMER Sara El-Gebali
15:15 - 15:30 Tea/coffee break  
15:30 - 17:00 InterPro Alex Mitchel
17:15 Bus to Cambridge Train Station  
Day 2 - How do I choose a "good" protein structure and what can I learn from it?
09:00 - 11:00 Introduction to protein structure and the PDBe David Armstrong
11:00 - 11:15 Tea/coffee break  
11:15 - 12:00 Making the most of the PDBe pages David Armstrong
12:00 - 12:45 Lunch  
12:45 - 15:00 PDBe tools (PISA and FOLD) David Armstrong
15:00 - 15:15 Tea/coffee break  
15:15 - 17:00 Electron Microscopy DataBank (EMDB) Ardan Patwardhan
17:15 Bus to Cambridge Train Station  
Day 3 - 
09:00 - 11:00 IntAct Birgit Meldal
11:00 - 11:15 Tea/coffee break  
11:15 - 12:30 Complex Portal Birgit Meldal
12:30 - 13:30 Lunch  
13:30 - 15:00 Reactome Steve Jupe
15:00 - 15:15 Tea/coffee break  
15:15 - 16:45 Reactome Steve Jupe
16:45 - 17:00 Wrap up and feedback Sarah Morgan
17:15 End of course; Bus to Cambridge Train Station