Stanford-Sweden multiresolution molecular modeling workshop

We are excited to announce our Stanford-Sweden summer modeling workshop, to be held in Uppsala 20-22 June. This workshop brings together scientists from the Bay Area, Sweden, and the wider world to discuss late-breaking research on simulation of macromolecules and complexes, spanning levels of resolution from coarse to fine. We will discuss structure prediction, dynamics, sampling, assembly, and aggregation from both a computational and experimental perspective. We will also give tutorials on simulation software, such as SimTK Simbody, DOCK_Blaster, and MMB/RNABuilder. Please post the attached flyer on your departmental email list, on physical bulletin boards, or otherwise circulate widely. Details on the program will be posted on our event page as they become available: http://xray.bmc.uu.se/flores/Stanford-Sweden-workshop-2011

Thanks, and hope you can make it!

Samuel Flores, Johan Åqvist, Erik Lindahl, and Michael Levitt

About the author: Samuel Flores (samuelfloresc AT gmail.com): I write easy to use multiresolution modeling software which helps predict how large biological molecules form and move. I and my collaborators have applied it to lots of problems, such as group I and group II intron structure, ribosome hybridization, and telomerase elongation. I’m also working on antibody design and other viral applications. Currently I’m extending my software, MMB, to handle huge complexes even more efficiently. A new feature called “physics where you want it” will let you apply a physics-based force field to a restricted region of your complex, e.g. an active site or interface, while treating the rest with coarser forces and kinematics. MMB will also start reading electron densities and other experimental data, expanding the types of constraints that can be used for modeling.


Rosetta Workshop

Rosetta Workshop

Rosetta Workshop

An Introductory Workshop to the Rosetta Protein Modeling Suite.


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Short Course: Crystallography for Modelers

The RCSB PDB will host a short course for practicing modelers looking for a better understanding of crystal structures and PDB data.

Dates: May 7 & 8 at Rutgers, The State University of New Jersey in Piscataway, NJ.

The target audience is PDB data users working in pharmaceuticals, biologicals, chemical industries, academia, and others who are looking to understand how to interpret in crystal structure data: possible problems, errors, and accuracy; how the data is determined and annotated; and what information and data is provided beyond atomic coordinates.

To learn more and register: Crystallography for Modelers

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3DSIG 2009 – Structural Bioinformatics and Computational Biophysics

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.


  • 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.


RosettaCon 2009

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

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Incorporating Flexibility Into Docking Using Normal Mode Analysis

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. 



The 2008 Computational Structural Bioinformatics Workshop

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.

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