Macromolecular Modeling Blog ™

This is the third post in the CAPRI series, summarizing the presentations of Jeffrey Gray, Zhiping Weng, and Miriam Eisenstein, as provided by the speakers. More to appear in the continuation of the series.
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PyRosetta Book

The Gray Lab at Johns Hopkins University has just released PyRosetta, a Python-based interactive platform for accessing the objects and algorithms within the Rosetta protein structure prediction suite.

In addition to the code, the Gray Lab has put together a book that leads the reader through basics of protein structure and energetics to applications in folding, refinement, docking and design. The focus is on enabling users to write custom scripts, so it includes material on Rosetta fundamentals and the appendices have a list of PyRosetta commands and a breakdown of the input files. The book was beta-tested by students during a course at JHU. The course is a series of workshops that teach how to measure and manipulate protein conformations, calculate energies in low- and high-resolution representations, fold proteins from sequence, model variable regions of proteins (loops), dock proteins or small molecules, design protein sequences, and build custom protocols for operations tailored to particular biomolecular applications

The book can be purchased through Lulu:

http://www.lulu.com/content/paperback-book/the-pyrosetta-interactive-platform-for-protein-structure-prediciton-and-design-a-set-of-educational-modules/7187010

or downloaded for free as pdf chapters from http://www.pyrosetta.org under the Tutorial link.

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 employed BioTeam (which Kraut consults for) to port Rosetta to the cloud. This is a fascinating article and certainly the Pfizer/BioTeam/Rosetta/Amazon synergy is a phenomenon on the bleeding edge.

I would add to the article that Jeffrey Gray at Johns Hopkins University was the lead developer of RosettaDock and RosettaAntibody. Rosetta has become synonymous with David Baker (and for good reason), but it is important to acknowledge continuing contributions to Rosetta outside of the Baker lab. Scientific collaborations can dissolve quickly when recognition is unevenly distributed, whether internally or as a result of outside perceptions (i.e. not as the result of any intentions by researchers in the collaboration).

If you use or write about Rosetta, please help us keep this unique collaboration going by acknowledging and citing the individual developers and researchers and their current labs!!!!