EMBO Practical Course: Computational structural biology - from data to structure to function
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Date:
Monday 16 April 2012Application opens:
Sunday 01 January 2012Application deadline:
Friday 24 February 2012Contact:
Frank O’DonnellRegistration closed
Overview
Is it right for me?
This course will teach computational aspects of protein structure determination, validation and analysis. Students will learn 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 I learn and what will it cover?
- Background to structural biology and the techniques involved: X-ray crystallography, Nuclear Magnetic Resonance Spectroscopy, Electron Microscopy and Small-angle X-ray scattering (SAXS)
- Experience in building a model from X-ray diffraction data, comparing and integrating different types of structural data, and the differences in interpretation.
- Deposition and retrieval of data to/from the PDB, validating structures, and how proteins can be classified into structural families and folds (specifically focusing on the CATH and Pfam databases).
- Comparing folds and multimeric assemblies, understanding the differences when dealing with membrane proteins
- Homology modelling of proteins that are difficult to determine experimentally.
- Analysis of protein structures, identifying what can and cannot be inferred and how to use the various tools.
- Predicting the function of proteins from structural data.
- Importance of protein structure and small molecule data in the development of drugs.
Additional information
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)
Programme
Draft Programme - (Subject to change)
| Time | Topic | Speaker |
|---|---|---|
| Day 1 - Monday 16 April 2012- Introduction, The wwPDB, Structure Determination Techniques, Structure validation | ||
| 09:00 - 09:30 | Welcome and Introduction | |
| 09:30 - 10:30 | Participant introductions and expectations | |
| 10:30 - 11:00 | Coffee break | |
| 11:00 - 11:45 | Background to protein structure and its determination | Victor Lamzin |
| 11:45 - 12:30 | Introduction to the wwPDB and the PDBe | Gerard Kleywegt |
| 12:30 - 13:30 | Lunch | |
| 13:30 - 14:30 | SAXS data | Maxim Petoukhov |
| 14:30 - 15:30 | NMR data | Aleksandras Gutmanas |
| 15:30 - 16:00 | Coffee break | |
| 16:00 - 17:00 | EM(DB) data | Ardan Patwardhan |
| 17:00 - 18:30 | Model Validation | Gerard Kleywegt, Sanchayita Sen |
| 18:30 - 18:45 | Wrap up session with questions | All Trainers |
| 19:30 - | Evening dinner at restaurant | |
| Day 2 - Tuesday 17 April 2012 - X-ray crystallography, Combining data from different techniques | ||
| 9:00 - 10:30 | Data Collection and model building | Victor Lamzin, Tim Wiegels and Santosh Panjikar |
| 10:30 - 11:00 | Coffee break | |
| 11:00 - 13:00 | Model building using AutoRickshaw, ARP/wARP, and other software | Victor Lamzin, Tim Wiegels and Santosh Panjikar |
| 13:00 - 14:30 | Lunch and Poster Session 1 | |
| 14:30 - 15:30 | Structure and function characterisation of macromolecular assemblies by a combination of experimental data, bioinformatics, and modelling techniques | TBC |
| 15:30 - 16:30 | Combining biochemical approaches, proteomics and cryo-electron microscopy to study the structure and function of large macromolecular assemblies | TBC |
| 16:30 - 16:45 | Coffee break | |
| 16:45 - 18:15 | Tools for low resolution model-building (including maps from EM) and for use in structure-based drug design | TBC |
| 18:15 - 18:45 | Open panel discussion and question session | |
| 19:30 - | Evening dinner at Wellcome Trust restaurant | |
| Day 3 - Wednesday 18 April 2012 - Small molecules, drug discovery and chemoinformatics | ||
| 09:00 - 10:30 | Chemistry in the PDBe using PDBeChem | Gaurav Sahni |
| 10:30 - 11:00 | Coffee break | |
| 11:00 - 12:00 | Drug discovery and ChEMBL | TBC |
| 12:00 - 13:30 | Small Molecule Identification | Victor Lamzin, Tim Wiegels |
| 13:30 - 14:15 | Lunch | |
| 14:15 - 16:00 | Small molecule docking using GOLD | Gary Battle |
| 16:00 - | Group Social event | |
| 20:00 - | Formal dinner at a Cambridge college | |
| Day 4 - Thursday 19 April 2012 - Protein classification and structure analysis (folds and assemblies), membrane proteins and homology modelling | ||
| 09:00 - 11:00 | Protein Folds and Families, CATH, SCOP and Pfam | Christine Orengo |
| 11:00 - 11:30 | Coffee Break | |
| 11:30 - 13:00 | Quaternary structure and fold comparison - PDBeFold/PDBePisa | Gaurav Sahni |
| 13:00 - 14:30 | Lunch and Poster Session 2 | |
| 14:30 - 15:30 | Membrane protein structure data | TBC |
| 15:30 - 16:00 | Homology Modelling (talk) | Gert Vriend |
| 16:00 - 16:30 | Coffee break | |
| 16:30 - 18:00 | Homology Modelling (practical) | Gert Vriend |
| 18:00 - 18:30 | Open panel discussion and question session: “Small molecules, drug discovery, chemoinformatics, docking, folds, families, assemblies, membrane proteins and homology modelling" | All Trainers |
| 19:30 - | Evening dinner at restaurant | |
| Day 5 - Friday 18 April 2012 - Interactions, Motifs, Patterns, and Function Prediction | ||
| 09:00 - 11:00 | Protein protein interactions and motifs | TBC |
| 11:00 - 11:30 | Coffee break | |
| 11:30 - 13:00 | Structural Motifs - PDBeMotif | Sanchayita Sen |
| 13:00 - 14:00 | Lunch | |
| 14:00 - 15:30 | Sequence and structure-based patterns - functional annotation and misclassification | TBC |
| 15:30 - 16:00 | Coffee break | |
| 16:00 - 17:30 | Protein function prediction | James Watson |
| 17:30 - 18:00 | Course closing comments and feedback session | |
| 18:00 - | Departures | |
Course Materials: Course_materials.zip
How to apply
Registration will be via a selection process therefore applicants should be aware that, in order to be considered for place on this course, they MUST complete the application page as well as submit a short CV, research interests and a letter of support from their supervisor or another senior co-worker. Incomplete applications will NOT be considered.
Information on how to submit this additional information is contained in your completed application for registration. Application registration closes 24 February 2012 (12 noon GMT). There will be a maximum of 25 participants on this course. Successful applicants will be notified by 2 March 2012 and will then be asked to confirm their place on the course by re-registering and paying the relevant registration fee.
Registration Fees:
The course registration fee will be £200 for applicants from academia.
N.B. You will not need to pay any money at the application stage. Payment will only be required once you have been accepted onto the course.
Registrants from Industry Fee = £1000.00
Please note that the registration fee includes:
- All meals (breakfast, lunch, dinner and refreshment breaks)
- Accommodation for 5 nights (check in Sunday 15 April 2012, check out Friday 20 April 2012), at the Wellcome Trust Conference Centre (www.wtconference.org.uk)
- Course materials
- Use of EBI IT Training Room computer during the 5 day course
NOTE: All delegates will need to arrange their own travel to and from the course.
Registration:
Registration is now closed.
Application deadline
24 February 2012
Organisers
James Watson
Rosemary Wilson
Gerard Kleywegt
Victor Lamzin - EMBL Hamburg, Germany
Christine Orengo - University College London, UK
Gert Vriend
Trainers
Victor Lamzin - EMBL Hamburg, Germany
Gerard Kleywegt - EMBL-EBI, UK
Maxim Petoukhov
Aleksandras Gutmanas - EMBL-EBI, UK
Ardan Patwardhan - EMBL-EBI, UK
Sanchayita Sen - EMBL-EBI, UK
Tim Wiegels
Santosh Panjikar
Gary Battle - EMBL-EBI, UK
Christine Orengo - University College London, UK
Nick Goldman - EMBL-EBI, UK
Gert Vriend