Macromolecular Modeling Blog ™

RosettaCon 2009 has ended just a few days ago.

This was a very exciting meeting, gathering almost all Rosetta developers from around the world, and representatives of the major industry licensees of Rosetta. The talks were quite diverse, ranging from new Rosetta protocols under development, applications with regards to numerous biological systems, and up to code architecture and future development of the code.

For scientists specializing in a specific field (such as computational structural biology – just off the top of my head) there are rare occasions in which meetings are dedicated entirely to their topic. This was such a conference! All through the three days of conference and one day of hiking, people had talked, discussed, brain stormed, ate, breathed, thought, swam, hiked, mingled and laughed protein structure. If the coffee break was drawn as a comic figure, with bubble clouds to depict thoughts and conversations, it would be a sea of alpha-helices, weird looking loops, rotamers, ligands and co-factors at interfaces, strange folds and stranger rainbow colored cartoon proteins. A modeler’s utopia.
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The Annual International Meeting of the Molecular Graphics and Modeling Society (MGMS) will take place in Erlangen, Germany from September 7th (registration and mixer) – 11th 2009.

The meeting will be preceded by the annual Molecular Modelling Workshop organised by the Molecular Graphics and Modelling Society – Deutschsprachige Sektion (MGMS-DS) from Sunday 6th to Monday, September 7th.

More Details: Modeling’09

An ISMB satellite meeting. Stockholm, June 27-28 2009.

3Dsig has established itself as a main event in the field of structural bioinformatics and computational biophysics since 2004. Amongst this year’s confirmed keynote speakers are Michael Levitt and Gunnar von Heijne. This is a unique event bringing together in one place the structural computational biology community. The program will be built around talks from accepted abstracts and invited speakers.

Keydates:

• February 16, 2009 – Registration opens for 3Dsig and ISMB/ECCB. 
• March 18, 2009 – Deadline for submitting an abstract to 3Dsig to be considered for oral presentation.
• April 2, 2009 – Deadline for travel fellowship application for the main ISMB/ECCB conference.

Disclaimer: We at “Rosetta Design Group“, use, develop and love Rosetta. That being said, you’d understand our amicable descriptions.

Rosetta is a modeling software suite that can do anything that have to do with modeling. From ab-initio folding and homology modeling, through protein-protein or protein-ligand docking, and to protein and enzyme design. Dozens of papers were written about its different protocols and about their application to specific biological systems. The secret for Rosetta’s success are the Rosetta Commons: a consortium, including over a hundred scientists from over 12 Universities which continues the ongoing research and development of the software.

Every summer the Rosetta Commons researchers, world experts on macromolecular modeling, as well as the people behind the code, gather at the Rosetta Conference (dubbed “RosettaCon”) to exchange ideas and discuss future plans.

We would like to invite you to RosettaCon to participate in workshops, seminars, and to have an opportunity to meet the Rosetta Commons researchers.
RosettaCon will take place during August 4-7 at the beautiful Sleeping Lady Mountain Retreat in Leavenworth, Washington, about 2.5 hours outside Seattle, set amid towering conifers and dramatic mountain scenery.

The Rosetta software is currently licensed for free to users at academic and nonprofit institutions and have over 2000 academic users in more than 32 countries. Commercial entities can use Rosetta by paying a license fee. Amongst past participants in these workshops are representatives of the big pharma companies and Rosetta’s licensees, RosettaCon Workshop 2008 was sponsored by Merck and Nanorex.

If you may be interested in joining us this year, please let me know, We will be sending the preliminary agenda to assess participants preferences in terms of workshop session contents and seminar topics, and to taylor them to your needs.

For more information and registration, email:

nir AT rosettadesigngroup.com

Incorporation of flexibility into docking simulations and accounting for backbone conformational changes during association is probably the toughest problem protein-protein dockers are facing today. Normal Mode Analysis is lately the answer of many groups to this problem. We hereby review two approaches of incorporating NMA into docking simulations, reflecting the induced fit vs. conformational sampling association mechanisms. 

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November 4-5, Philadelphia, PA, USA.

The 2008 Computational Structural Bioinformatics Workshop (CSBW) will be held in conjucntion with the IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2008) The rapid accumulaiton of macromolecular structures presents a unique set of challenges and opportunities in analysis, modeling and prediction of mcrommolecular structures and interactions. This workshop aims to bring together researchers with expertise in bioinformatics, computational biology, structural biology, data mining, optimization and high performance computing to discuss recent results, new techniques and open research problems in computational structural bioinformatics. Workshop website.