Macromolecular NMR assignment with CcpNmr Analysis

In cooperation with the Portuguese NMR Network and the CCPN consortium.

   Deadline for applications: May 19th 2010
   Notification of acceptance dates:
        EARLY:May 14th
        NORMAL: May 21st 2010
   Course date: May 31st - June 4th 2010


Manolis Matzapetakis got his Ph.D. in Biological Chemistry (denovo Protein design and NMR) from the University of Michigan in Ann Arbor and then did his PostDoc at the Centrer of Magnetic Resonance (CERM) in Florence, Italy, working on the NMR of large proteins. He is currently the head of the lab of Biomlecular NMR group at ITQB in Oeiras, Portugal and his interests are in the fields of structural proteomics and ferrous homeostasis. He is interested in high-throughput structure depermination by NMR, using rapid data acquisition techniques as well as the study of protein-protein interactions.

Affiliation: Instituto de Tecnologia Química e Biológica, Oeiras, PT

Pedro Lamosa has a degree in Biochemistry from the University of Lisbon, and a PhD in Biochemistry (Protein structure and protein dynamics by NMR) from the New University of Lisbon. He is currently the manager of CERMAX (Centro de Ressonância Magnética António Xavier). Having devoted his research to the adaptation of microorganisms to high temperatures, Pedro Lamosa has mainly used NMR to study protein stabilization by compatible solutes. These studies have focused in the discovery and structure determination of novel compatible solutes accumulated by hyperthermophiles, and their action upon protein structure and protein dynamics.

Affiliation: Instituto de Tecnologia Química e Biológica, Oeiras, PT

Rasmus Fogh has a masters degree in Chemistry (NMR spectroscopy) from the University of Copenhagen, and a PhD in Biochemistry (Protein structure determination by NMR) from the University of New South Wales. He has worked on protein structure determination by NMR in the laboratories of Robert Kaptein in Utrecht and Ernest Laue in Cambridge, and on pharmaceutical NMR at GlaxoWellcome, Verona. He is now in the group of Ernest Laue, Biochemsitry, University of Cambridge, where he has been working on the CCPN project for the past ten years, mainly on the CCPN data exchange standard for macromolecular NMR and the Memops code generation machinery. His main interests are data modelling, NMR software, and protein NMR spectroscopy.

University of Cambridge, Cambridge, UK

Tim Stevens is one of the core developers of the CCPN project. He is one of the main authors of CcpNmr Analysis; CCPN's spectrum visualisation, assignment and analysis program. He lectures bioinformatics to 3rd and 4th year undergraduates taking Biochemistry as part of the Natural Sciences Tripos at the University of Cambridge. Tim also does a significant amount of teaching for practical, computational classes within the School of Biology. These range from undergraduate cellular biology to computer programming in Python, as well as more specialist courses for CCPN. He obtained his degree and PhD in the Department of Biochemistry at the University of Cambridge, where he still resides working as part of the CCPN team. His research interests include the bioinformatics of transmembrane proteins, the automation of NMR resonance assignment and protein structure calculation.

University of Cambridge, Cambridge, UK

Marc van Dijk obtained his degree in Biology at Utrecht University in the Netherlands, specializing in molecular cell biology. He obtained his PhD degree at the NMR Spectroscopy Department at the same university under the supervision of Prof. Alexandre Bonvin where he extended the labs well-known macromolecular docking program HADDOCK to deal with protein-DNA complexes. Apart from his main research interest in the field of docking he worked on integration of HADDOCK into the CCPN data model en contributed to the development of the HADDOCK web server. Currently he is working together with the CCPN team on further development of the analysis software suite. He has taught HADDOCK training courses on several occasions.

Bijvoet Center for Biomolecular Research
Utrecht University
The Netherlands

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.

Course Pre-requisites:

Familiarity with NMR spectroscopy and its terminology. Basic protein biochemistry.

Detailed Program

Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:  April 19th 2010