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From WikiGagneLague

If you came here looking for a specific guide, feel free to jump directly to the scientific and technical topics section; otherwise, read on to learn about our research groups and this Wiki.

Latest news

• March 10th, 2011 : 55th Biophysical Society Annual Meeting in Baltimore. Great conferences!

• May 11th, 2010 : Sébastien Morin's thesis defence..!

• A few of us recently attended the 53rd Biophysical Society Annual Meeting in Boston. Sébastien was awarded at the SRAA poster competition ! Conferences were great ! We had a great time with Michèle Auger's folks and Anika ! Everyone enjoyed this event !

• Pierre-Yves Savard's thesis defense was on December 15th, 2008 ! This was the first thesis presented in the Gagné lab. Pierre-Yves's thesis is titled : Caractérisation structurale et dynamique de la beta-lactamase TEM-1 de la bactérie Escherichia coli par RMN liquide. Congratulations PY !

• The 10th β-Lactamase Meeting, held in Eretria, Greece, from June 1 to 3, 2008, was an extremely interesting event. Photos from the meeting and my subsequent trip in Greece can be found on the Web and in our photo repository (directory greece-2008). The file description.txt (which you will find alongside the photographs) contains a short description of each photo.

Research groups members should check the current events page for more details. Older events and photos can be found in the archived news section.

What is the Wiki Gagné • Lagüe?

This Wiki is a joint project of two research groups from Laval University's Departement of Biochemistry and Microbiology. Our two groups work on structural biochemistry and are members of the PROTEO organisation which promotes research on protein function, structure and engineering.

Altough you will find much information about our research groups on these pages, the main purpose of this WiKi is to serve as a repository of theoretical and practical information about NMR spectroscopy, protein overexpression and purification, molecular dynamics, QM/MM, structural biochemistry, UNIX/Linux computer systems and other topics of general interest to researchers and their students. You will find a number of guides, tutorials and some teaching material on these themes in the scientific and technical topics section.

Professor Stéphane Gagné's research group uses NMR spectroscopy as its principal tool for studying the structure and dynamical properties of proteins and peptides. Professor Patrick Lagüe's group uses computational biology techniques such as molecular dynamics (MD), quantum mechanics (QM, QM/MM), docking and quantitative structure-activity relationship (QSAR) methods for investigating a wide range of phenomena such as lipid-peptide interactions, protein network cavities and protein dynamics.

Biological systems currently studied include class A β-lactamases TEM-1 and PSE-4 (along with variants and chimeras of these two model proteins), truncated hemoglobins, aminocyl-tRNA-synthetases (such as GluRS, its substrates and inhibitor compounds) and virus capside structual proteins.

Both groups promote the use of free software in scientific research (and computing in general), as symbolised by our Wiki logo, the now famous Tux, the Linux mascot. The essential amino acid phenylalanine appearing on Tux's tummy reminds of biochemistry. A nuclear spin and a binary number symbolise NMR spectroscopy and bioinformatics. Our favorite Linux flavour is the Gentoo Linux metadistribution, which we can customise to fit varied needs: we run Gentoo on laptop computers, graphical workstations, headless servers and high performance computing (HPC) clusters of computers. We contribute to the Gentoo community through involvement as developers and extensive testing in production environments.

Our current equipment includes a 600 MHz NMR spectrometer and a 130 core HPC cluster. Our NMR spectrometer (a Varian Inova model) is equiped with a cryoprobe for increased resolution. The research building we work at was designed to allow the installation of another high-field instrument in the near future. Our cluster is made of heterogenous computer nodes: 25 2.2 GHz AMD Opteron dual-processor nodes, 12 3.0 GHz Intel Xeon dual-core dual-processor nodes and 4 2.66 GHz Intel Xeon quad-core dual-processor nodes. Hardware and software support is provided by Cyberlogic.

Learn more about students, professors and professionals in our research groups, our research projects, software projects and publications by checking the relevant sections of this Wiki.

Also check out our favourite Internet resources page, where you will find links to online databases, our favourite software home pages, etc.

Pages listed in the for the group section of the navigation bar (on the left) are likely to be of interest only to members of the research groups. Other sections (particularily the scientific and technical topics) were written in the hope that they would be interesting for anyone working on structual biochemistry or with UNIX/Linux computer systems.