Macromolecular Modeling Blog ™

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.

We recently saw these posts reporting that Warren DeLano passed away on Tuesday:

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=CCP4BB;19EK9w;20091105105413-0800

http://www.macresearch.org/memoriam-warren-l-delano

This is a terrible tragedy and our hearts go out to his family and friends. He was a truly incredible person whose work with PyMOL changed the face of molecular modeling. He also had a huge personal impact on our community. He was dedicated to science and dedicated to making the world a better place through his example and by the personal way he interacted with everyone.

When I was considering starting the Rosetta Design Group a few years back, I asked Warren for some advice by email. He promptly called and we talked for a few hours. After our conversation I reflected on how much his call and advice meant to me, and hoped that I would act as he did in the same situation.

May his example, memory, and code live on forever.

My jaw dropped when I saw this. Hilarious. Scary. So true.

Molecular Modelers have Aspergers

Its from: http://en.wikipedia.org/wiki/Asperger_syndrome

A variety of groups have sprung up on LinkedIn that may be of interest to macromolecular modelers. In these groups, there are job postings, literature reviews and notices, discussions, and more. Below is a list of groups that we have joined. Do you know of a group that is not listed below?

Antibody Network

Biotech & Pharma Professionals Network

Computational Biology

Protein engineering

Structure-Based Drug Design

Molecular Modeling in Life Sciences

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!!!!