EMBO Practical Course: Computational structural biology - from data to structure to function
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.
| Time | Topic |
|---|---|
| Day 1 - Mon 14 Nov 2011 - Introduction, The wwPDB, Structure Determination and Model Building | |
| 08:45 | Shuttle bus from Holiday Inn Express - Whittlesford to EBI |
| 09:00 - 09:30 | Welcome and introduction to the EBI (Janet Thornton- EMBL-EBI) |
| 09:30 - 10:00 | Participant introductions and expectations |
| 10:00 - 11:00 | Background to protein structure and its determination (Santosh Panjikar - EMBL-Hamburg) |
| 11:00 - 11:30 | Coffee break |
| 11:30 - 12:30 | Talk: Introduction to the wwPDB and the PDBe. Practical searches of the wwPDB and extraction of data. Use of molecular graphics viewers (Gerard Kleywegt - EMBL-EBI) |
| 12:30 - 13:30 | Practical: Introduction to the wwPDB and the PDBe. Practical searches of the wwPDB and extraction of data. Use of molecular graphics viewers (Gaurav Sahni, Martyn Symmons - EMBL-EBI) |
| 13:30 - 15:00 | Lunch and poster session 1 |
| 15:00 - 16:00 | Talk and Practical: Data Collection and model building (Tim Wiegels, Santosh Panjikar - EMBL-Hamburg) |
| 16:00 - 16:30 | Tea break |
| 16:30 - 18:30 | Practical Session: Model building using AutoRickshaw, ARP/wARP, and other software (Tim Wiegels, Santosh Panjikar - EMBL-Hamburg) |
| 18:30 - 18:45 | Wrap up session and questions |
| 18:45 | Shuttle bus from EBI to Holiday Inn Express - Whittlesford |
| 19:30 | Dinner in Red Lion Whittlesford (next door to Holiday Inn Express) |
| Day 2 - Tue 15 Nov 2011 - Other Structure Determination Techniques, Structure validation | |
| 08:25 | Shuttle bus from Holiday Inn Express - Whittlesford to EBI |
| 08:45 - 10:45 | Talk and Practical: SAXS data (Maxim Petoukhov - EMBL-Hamburg) |
| 10:45 - 11:00 | Coffee break |
| 11:00 - 11:45 | Talk: NMR data (Aleksandras Gutmanas - EMBL-EBI) |
| 11:45 - 12:30 | Practical: NMR data (Aleksandras Gutmanas, Pieter Hendrickx - EMBL-EBI) |
| 12:30 - 13:30 | Lunch |
| 13:30 - 14:15 | Talk: EM(DB) data (Ardan Patwardhan – EMBL-EBI) |
| 14:15 - 15:00 | Practical: EM(DB), viewers, combining PDB and EMDB data (Ardan Patwardhan, Ingvar Lagerstedt, Eduardo Sanz Garcia – EMBL-EBI) |
| 15:00 - 15:15 | Tea break |
| 15:15 - 16:00 | Talk: Model Validation (Swanand Gore - EMBL-EBI) |
| 16:00 - 16:45 | Practical: Model Validation (Swanand Gore, Gaurav Sahni - EMBL-EBI) |
| 16:45 - 17:15 | Open panel discussion and question session: Structure determination techniques, model building and validation, the PDB (All Trainers) |
| 17:20 | Bus departs to Cambridge |
| 17:45 | Social drinks in historic Eagle pub followed by free time in Cambridge |
| 20:00 - 22:30 | Formal dinner at a Jesus College, Cambridge |
| Day 3 - Wed 16 Nov 2011 - Small molecules, drug discovery and chemoinformatics | |
| 08:45 | Shuttle bus from Holiday Inn Express - Whittlesford to EBI |
| 09:00 - 09:45 | Talk: Chemistry in the PDBe using PDBeChem (Sanchayita Sen- EMBL-EBI) |
| 09:45 - 10:30 | Practical: Chemistry in the PDBe using PDBeChem (Sanchayita Sen, Matthew Conroy- EMBL-EBI) |
| 10:30 - 11:00 | Coffee break |
| 11:00 - 12:00 | Short Talk and Practical: Chemoinformatics and ChEBI (Paula de Matos- EMBL-EBI) |
| 12:00 - 13:00 | Short Talk and Practical: Drug Discovery and ChEMBL (Louisa Belliss- EMBL-EBI) |
| 13:00 - 14:30 | Lunch and poster session 2 |
| 14:30 - 16:00 | Talk and Practical: Small molecule identification (Tim Wiegels - EMBL-Hamburg) |
| 16:00 - 16:30 | Tea Break |
| 16:30 - 18:00 | Practical Session: Small molecule docking using GOLD (Gary Battle - CCDC) |
| 18:00 - 18:30 | Wrap up session and questions (All Trainers) |
| 19:30 | Dinner in Red Lion Whittlesford (next door to Holiday Inn Express) |
| Day 4 - Thu 17 Nov 2011 - Protein classification and structure analysis (folds and assemblies), membrane proteins and homology modelling | |
| 08:45 | Shuttle bus from Holiday Inn Express - Whittlesford to EBI |
| 09:00 - 11:00 | Talk and Practical: Protein Folds and Families, CATH, SCOP and Pfam (Christine Orengo - UCL) |
| 11:00 - 11:30 | Coffee break |
| 11:30 - 12:15 | Talk: Quaternary structure and fold comparison - PDBeFold/PDBePisa (Martyn Symmons - EMBL-EBI) |
| 12:15 - 13:00 | Talk and Practical: Quaternary structure and fold comparison - PDBeFold/PDBePisa (Martyn Symmons, Matthew Conroy - EMBL-EBI) |
| 13:00 - 14:00 | Lunch |
| 14:00 - 15:30 | Lecture and Practical: Membrane protein structure data (Arne Elofsson) |
| 15:30 - 16:00 | Talk: Homology Modelling – GPCRs (Gert Vriend - CMBI) |
| 16:00 - 16:30 | Tea break |
| 16:30 - 18:00 | Practical: Homology Modelling – GPCRs (Gert Vriend - CMBI) |
| 18:00 - 18:45 | Open panel discussion and question session Small molecules, drug discovery, chemoinformatics, docking, folds, families, assemblies, membrane proteins and homology modelling (All Trainers) |
| 19:00 | Shuttle bus from EBI to Holiday Inn Express - Whittlesford |
| 20:00 | Dinner in Red Lion Whittlesford (next door to Holiday Inn Express) |
| Day 5 - Fri 18 Nov 2011 - Interactions, Motifs, Patterns, and Function Prediction) | |
| 08:45 | Shuttle bus from Holiday Inn Express - Whittlesford to EBI |
| 09:00 - 11:00 | Talk and Practical: Protein protein interactions and motifs (Rob Russell) |
| 11:00 - 11:30 | Coffee break |
| 11:30 - 12:15 | Talk: Structural Motifs - PDBeMotif (Sanchayita Sen - EMBL-EBI) |
| 12:15 - 13:00 | Practical: Structural Motifs - PDBeMotif (Sanchayita Sen, Gaurav Sahni - EMBL-EBI) |
| 13:00 - 14:00 | Lunch |
| 14:00 - 15:30 | Talk and Practical: Sequence and structure-based patterns - functional annotation and GPCRs (Teresa Attwood - University of Manchester) |
| 15:30 - 16:00 | Tea break |
| 16:00 - 17:30 | Talk and Practical: Protein function prediction (Roman Laskowski, James Watson - EMBL-EBI) |
| 17:30 - 18:00 | Course closing comments and feedback session |
| 18:00 | Departures (participants to make their own travel arrangements) |
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 30 September 2011 (12 noon GMT). There will be a maximum of 25 participants on this course. Successful applicants will be notified by 7 October 2011 and will then be asked to confirm their place on the course by re-registering and paying the relevant registration fee.
Registration Fees:
Academic Registration Fee = £100.00
Industry Registration Fee = £1000.00
Please note that the registration fee includes:
- All meals (breakfast, lunch, dinner and refreshment breaks)
- Accommodation for 5 nights (check in 13 November 2011, check out 18 November 2011), in the Holiday Inn Express, Duxford (http://www.hiexpress.com/hotels/gb/en/cambridge/cbgdk/hoteldetail)
- Transport to/from the accommodation to/from the EBI during the 5 days
- 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 is now closed
Course materials can be found at the following links:
/training/sites/ebi.ac.uk.training/files/materials/2011/111114_structures/day1a.zip
/training/sites/ebi.ac.uk.training/files/materials/2011/111114_structures/day1b.zip
/training/sites/ebi.ac.uk.training/files/materials/2011/111114_structures/day2.zip
/training/sites/ebi.ac.uk.training/files/materials/2011/111114_structures/day3.zip
/training/sites/ebi.ac.uk.training/files/materials/2011/111114_structures/day4.zip
/training/sites/ebi.ac.uk.training/files/materials/2011/111114_structures/day5.zip
/training/sites/ebi.ac.uk.training/files/materials/2011/111114_structures/pdbe_education.zip