Macromolecular Modeling Blog ™

Rosetta 3.2 is the first rosetta release in over a year and is chock-full of new features. Get your (free for academia) copy at: www.rosettacommons.org/software and find the new and improved documentation at: www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide

What’s new in Rosetta 3.2 ?

“Automatic” Comparative Modeling: build structural models of proteins using one or more known structures as templates for modeling.

Flexible Peptide Docking: create high-resolution models of complexes between flexible peptides and globular proteins, starting from approximate, coarse-grain models.

Symmetric Docking: predict the structure of symmetric homooligomeric protein assemblies starting from the structure of a single subunit. The relative subunit orientation and conformations of side-chains are simultaneously optimized for a symmetric protein assembly.

RosettaMatch Application: search through a protein backbone (“scaffold”) to find positions where a binding site for a desired small molecule (or biomolecule, in the more general case) target can be introduced.

Molecular Replacement: solve difficult molecular replacement problems. It will generally be used alongside the molecular replacement software Phaser.

Sequence Tolerance: perform specificity prediction and library design (i.e. for phage display, yeast display, or other selection techniques).

In a post yesterday on the Bleeding Edge Biotech Blog, Adam Kraut gives an expanded version of his article for Bio-IT World entitled Antibody Docking on the Amazon Cloud describing how Pfizer is leveraging the power and flexibility of cloud computing to run antibody docking simulations using Rosetta. Pfizer with help from the Rosetta Design Group (that’s us) developed an antibody modeling and docking workflow, which they then scaled up and tested on the cloud with help from BioTeam (which Kraut consults for and talks about in his post). This is a fascinating article and certainly the Pfizer/RDG/BioTeam/Rosetta/Amazon synergy is a phenomenon on the bleeding edge.

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