Hands-on training at EBI - EMBO Practical Course 'Computational aspects of protein structure determination and analysis: from data to structure to function'

Title: EMBO Practical Course 'Computational aspects of protein structure determination and analysis: from data to structure to function'
Date: 6-10 September 2010
Venue: EMBL-EBI, Hinxton, Cambridge, CB10 1SD, UK
Organisers: James Watson, Rosemary Wilson
Admin Support: Holly Foster, Alison Barker & Frank O'Donnell
Registration Opens: 6 March 2010
Registration Deadline: 23 July 2010 - 12 noon (GMT)
Acceptance Notification Date: 30 July 2010 - 12 noon (GMT)

Main Sponsor

Scientific Committee

• Gerard Kleywegt (EMBL-EBI, Wellcome Trust Genome Campus, UK)
• Victor Lamzin (EMBL Hamburg, Germany)
• Christine Orengo (University College London, UK)
• Gert Vriend (CMBI, NCMLS, Nijmegen, Netherlands)

Course Overview

Is it right for me?

The course will teach computational aspects of protein structure determination, validation and analysis. It will cover the background of X-ray crystallography, Nuclear Magnetic Resonance Spectroscopy, Electron Microscopy and Small-angle X-ray scattering (SAXS) and provide hands-on experience in building a model from X-ray diffraction data, comparing and integrating different types of structural data, and the differences in interpretation. Subsequent days will teach the students to critically examine and validate data from the Protein Data Bank and use a variety of analysis tools to identify similarities that can help identify function. The course will also provide an introductory session to homology modelling for use with proteins less amenable to structure determination. Finally, the importance of protein structure to drug development will be illustrated with a day focussing on protein interactions, small molecules, chemoinformatics and docking.

The course is aimed at PhD students and post-docs working on the collection and analysis of protein structure data. The goal is to provide them with insight into the protein structure determination process, how to critically assess the quality of data from models and also provide expertise in the analysis of protein structure data with a view to predicting protein function.

What will it cover?

• Day 1: The first day of the course will aim to bring all attendees and speakers together to network and get to know their areas of expertise and interests. The poster session with buffet lunch on this day will efficiently bring all participants together and let the trainers and speakers identify the most suitable focal points for subsequent discussions and examples used in their training sessions. The morning of the first day will, through a series of lectures, provide the background to structural biology, an introduction to NMR data, the Protein Data Bank (PDB) and the computational techniques that will be used in the afternoon's practical sessions. The practical sessions will take raw crystallography data and teach the students how to analyse it in order to construct a model of the protein structure.
• Day 2: This day will continue with sessions demonstrating different types of experimental data (SAXS and EM). The remainder of the day will investigate validation of structures, and how proteins can be classified into structural families and folds (specifically focusing on the CATH and Pfam databases). The day will end with an open discussion led by the trainers on aspects of protein structure determination, validation and family/fold groupings that the students wish to elaborate on and discuss in more depth.
• Day 3: The course now moves on to comparing folds and multimeric assemblies, understanding the differences when dealing with membrane proteins and, finally, using what has been discussed on days 2 and 3, will turn to homology modelling of proteins that are difficult to determine experimentally. The afternoon of this day will involve a trip into the city of Cambridge to take a tour and (weather permitting) take part in a social activity: punting on the river Cam through the historic colleges of the University. This will be followed in the evening by a formal dinner in one of the University colleges.
• Day 4: The focus of the course now moves on to the analysis of protein structures, identifying what can and cannot be inferred and how to use the various tools. This will begin with a session on structural motifs in proteins and how they differ from the sequence patterns more commonly used. This will then lead on to sessions exploring enzymes and active sites and finally, in the afternoon, all of the different approaches identified in the course will be looked at for predicting the function of proteins from structural data. At the end of the day the course will round up with the second open discussion session, led by the trainers again, on aspects of protein structure analysis and function prediction that the students wish to discuss further. This open discussion session will also be used to gain an insight into the hopes of the students for the final day of the course.
• Day 5: The final day will focus on the importance of protein structure and small molecule data in the development of drugs. The day will start with a lecture on protein-protein and protein-small molecule interactions, then move onto looking at chemistry in the PDB, identifying small molecules and chemical entities and finally onto drug discovery using protein structures and docking compounds to them.

Programme

Registration and Payment

Important Information

• Relevance of the candidate’s research interests and current work to the course objectives.
• Scientific excellence of the previous research
• Letter of support from the candidate’s supervisor or another senior co-worker.
• Geographical distribution
• Recommendations from EMBO

Participants at early stages of their career will be accepted if they can demonstrate the relevance of their work to the objectives of the course. Participants who have used a systems-based approach to understanding a biological problem will be preferred. The last Hands on session will concentrate on the participants specific research cases, so participants are encouraged to bring data from their own research. However, in order to make these feasible, participants will be asked upon acceptance to prepare their data in specific format (and to a specified maximum size).

Information for commercial applicants

Our course funders request that we charge a higher registration fee to commercial delegates, and may also set some limits on the number of commercial delegates at each course; Please see the section on costs below for details.

Registration:

Costs:

Registration Fee = £50.00

Commercial/SME Registration Fee =
£900.00 (1000 EURO)
EBI Industry Programme Member Registration Fee = £375.00 (accommodation costs)

Please note that the registration fee includes single accommodation for in Cambridge between 5-10 September 2010, all meals during the course, transport to and from Cambridge and the EBI on each of the course days and all workshop materials.

Invited Speakers and Trainers

• Janet Thornton, EMBL-EBI, UK
• Victor Lamzin, EMBL-Hamburg, Germany
• Santosh Panjikar, EMBL-Hamburg, Germany
• James Watson, EMBL-EBI, UK
• Maxim Petoukhov, EMBL-Hamburg, Germany
• Christoph Best, EMBL-EBI, UK
• Wim Vranken, EMBL-EBI, UK
• Roman Laskowski, EMBL-EBI, UK
• Gert Vriend, Centre for Molecular and Biomolecular Informatics, Nijmegen, Netherlands
• Gerard Kleywegt, EMBL-EBI, UK
• Barbara Beuth, EMBL-EBI, UK
• Miriam Hirshberg, EMBL-EBI, UK
• Gaurav Sahni, EMBL-EBI, UK
• Sanchayita Sen, EMBL-EBI, UK
• Christine Orengo, University College London, UK
• Rob Finn, Wellcome Trust Sanger Centre, UK
• Gemma Holliday, EMBL-EBI, UK
• Nicholas Furnham, EMBL-EBI, UK
• Marialuisa Pellegrini-Calace, EMBL-EBI, UK
• Michael Kuhn, Biotechnology Center (BIOTEC) of the Technische Universitat Dresden, Germany
• Christoph Steinbeck, EMBL-EBI, UK
• Paula De Matos, EMBL-EBI, UK (t.b.c.)
• John Overington, EMBL-EBI, UK