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Biological Sequence Analysis:

Exploring Modular Protein Architecture

ENSEIRB, Bordeaux, France. June 13th-15th, 2007

Exploring Modular Protein Architecture is a 3-Day course to introduce experimental scientists to a range of tools that help to identify the individual modules that make up a protein sequence.

This page is being developed with key details for the course, including a summary of what the course is about and how to apply.

What is the rational behind the course?

Over the last few years a new paradigm has been emerging concerning the nature of Eukaryotic regulatory proteins. That is to say, we have begun to understand in outline (but not at all well in detail) what regulatory proteins look like and how they work. The nice neat globular protein view expounded by biochemical and cell biological textbooks does not work well here. Instead, many proteins have a remarkable number of architecture modules - including long natively disordered segments and short linear motifs that are awkward to investigate computationally and experimentally. The course will set the scene by introducing the biological concepts behind these architecture modules and provide extensive hands-on application of the relevant bioinformatics tools with appropriate example proteins. The power - but also the limitations, which remain substantial - of the currently available software will be examined. The course will be judged to have succeeded if experimental researchers return to their institutes better equipped to dissect the architecture of proteins involved in cell signalling and regulation.

The Main Bioinformatics Tools covered

  1. The basic tools of the trade. Database retrieval with SRS and BLAST;
  2. Tools for protein modules. Domain servers e.g. Pfam, SMART; Disorder servers e.g. GlobPlot, IUPred; Linear motif resources e.g. ELM, Phospho.ELM, DiLiMot; Cinema/Utopia content integration; Looking at 3D structures with PyMol.
  3. Resources for protein interactions e.g. STRING, IntAct, Mint.

Course Schedule

General structure of a course day

09:00 - 18:00 Course runs through the day

11:00 Coffee Break / 13:00 - 14:00 Buffet Lunch / 16:00 Coffee Break

Dinner reservation for 20:00

Note: the Poster Session will take place 13:30 - 15:00 on Wednesday 13th June. We may look out for suitably modular proteins that are worth discussing with the course participants.

Wednesday 13th June

  1. Welcome.
  2. Introduction to Modular Protein Architecture and its role in cell regulation: (1 hour talk) Toby Gibson
  3. Introduction to Bioinformatics and Biological Databases: Aidan Budd
  4. Keyword Searching of Databases - SRS: Venkata Pardhasaradhi Satagopam and Aidan Budd
  5. Sequence Database Similarity Searches - BLAST: Niall Haslam and Aidan Budd

Thursday 14th June

  1. Predicting Globular Domains - PFAM, SMART, CDD: Niall Haslam and Aidan Budd
  2. Predicting Native Disorder - IUPred, DisProt, GlobPlot: Toby Gibson, Niall Haslam, and Aidan Budd
  3. Identifying potential ELMs - ELM, PhosphoELM: Toby Gibson and Aidan Budd
  4. Web Services/Utopia/Cinema: James Sinnott, Dave Thorne, and Aidan Budd

Friday 15th June

  1. Structure of Protein-Protein Interactions - PyMOL, PDB, MSD: Sebastien Fribourg
  2. Protein-Protein Interactions - STRING, MINT: Michael Kuehn and Aidan Budd
  3. Bring Your Own Sequences - A chance to work through sequences of particular interest to you while the teachers are still present.

Data and sequences for exercises

Links to relevant websites and resources

Notes for teachers on possible datasets etc.

Questions for evaluation form

The Trainers

Aidan Budd is a staff member working in Toby Gibson's group in the EMBL, Heidelberg

Toby Gibson is a group leader at the EMBL in Heidelberg

Niall Haslam is a postdoc working in Toby Gibson's group in the EMBL, Heidelberg

Venkata Satagopam is a scientific programmer working in Reihnhard Schneiders group in the EMBL, Heidelberg

Michael Kuhn is a PhD student working in Peer Bork's group in the EMBL, Heidelberg

Sebastien Fribourg is a group leader at the IECB in Bordeaux.

James Sinnott works as a research associate in the Advanced Interfaces Group in Manchester University.

Dave Thorne is a PhD student working in the Advanced Interfaces Group in Manchester University.

Who we are

The course is conceived as part of the outreach programme of the FP6 EMBRACE project from which it receives sponsorship. The main organisers are from Toby Gibson's group at EMBL. Aidan Budd is the group's course organiser and will do a lot of the organisation. The Gibson group work closely with David Sherman and Antoine de Daruvar in Bordeaux on the Fp6 ProteomeBinders project and they have offered to be the hosts at ENSEIRB the Engineering school in Bordeaux. Sandrine Palcy has previous training experience and will be helping with the organisation in Bordeaux. We have also invited several experts to teach particular parts of the course.

Applying to the training workshop

Email your application to Nelly van der Jagt at EMBL. jagt at embl dot de tel +49-6221-387361. Scientific queries should be directed to one of the organisers e.g. Aidan Budd or Toby Gibson.

Applications will be evaluated and accepted primarily on a first come - first served basis. There is a maximum of 25 places. There is a course fee of Euro 200 which covers the workshop, lodging and food. Any requests to waive the course fee will be entered into a small pool and considered one month before the course and may limit chances of acceptance.

Please supply full details of who you are, what you do and where you do it. You are not expected to be a computer expert but it is important that you list your computational experience so we can tune the course as needed. e.g. if you have scripting experience say so.

There will be a poster session. Please provide your preliminary title. The poster size should not exceed 2m X 1m 60cm.

To keep costs down, expect to share a room. Notify any special requirements.

Travel and accomodation details will be placed and revised here.

EMBRACE will cover the cost of accomodation for the nights of Tuesday 12th to Thursday 14th. The course will finish early afternoon on Friday (ending with some flexi-time to do your own favourite sequences). Therefore you should book to travel out on the Tuesday and return Friday night. If you want to stay into the weekend (after all Bordeaux is a very nice city), you will cover the cost of the extra nights accommodation yourself.

-- TobyGibson - regular updates from 14 May 2007, started 02 Mar 2007

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