Macromolecular Modeling Blog ™

As from next week, the RCSB PDB will provide web widgets – small bits of code, which provide PDB functionality that you can embed in your own website. All of the widgets that are provided are 100% self contained JavaScript files and will be maintained by the RSCB PDB. We’ve taken some of those widgets for a test drive.

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Several positions for molecular modelers have recently came to our attention. We thought some of our readers might express interest in these opportunities. If you find this type of service helpfull/annoying please let us know in the comments. If you wish to post available positions in the molecular modeling field please contact us.

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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.

After a long break, the molecular modeling literature digest is back with ~50 recent publication which we believe would be of interest. As usual you are most welcome to add relevant publications or suggest specific papers for us to focus on.

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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.