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Analysis course, April 2008
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CcpNmr Course, Oeiras Portugal
| What | Meeting |
|---|---|
| When |
2010-05-31 09:30
to 2010-06-04 16:00 |
| Where | Instituto Gulbenkian de Ciência, Oeiras, Portugal |
| Contact Name | Pedro Fernandes |
| Attendees | Rasmus Fogh, Tim Stevens, Marc van Dijk |
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Macromolecular NMR assignment with CcpNmr Analysis in cooperation with the Portuguese NMR Network.
Course Description
The course sets off with a first day of introduction in which people with less familiarity with Biomolecular NMR will be brought up to speed with the rest of the group. This has the additional advantage of making the terminology uniformly understood by all the participants. The course participants will then be introduced to the CCPN package that will be used throughout the course. We will use it in all the steps of NMR analysis and also as a platform to launch various programs and tools , like ARIA, DANGLE and CING. The aim is that by the end of the 3 to 4-day session the participants will have a working familiarity with CCPN, together with some of its connected software, and an understanding of the NMR data pipeline from processed spectra to macromolecular structure. This part of the course can be broken down into several components:
- The setup and navigation of multi-dimensional processed NMR spectra
- Peak picking and connecting peaks in related spectra
- Semi-automated and automated assignment of protein sequence
- Extraction of data for efficient relaxation rate analysis
- Generation of dihedral angle restraints using DANGLE
- Generation of NOE-derived distance restraints
- Structure calculation using a web service running ARIA
- Restraint violation analysis
- Structure validation using the iCING web service
- Writing simple Python scripts to manipulate CCPN data
In the last day will also cover HADDOCK (the principles and practical application), the integration of HADDOCK in CCPN and we will finish the day with a discussion of the eNMR project and the services available on the eNMR GRID.