News From Rosetta@home

I am taking the release of a paper to highlight Rosetta@home, BOINC, and World Community Grid

Rosetta@home is a colossally important project running on BOINC software.

Projects running BOINC software are part of what is called Public Distributed Computing. This process runs on the unused CPU cycles of about 275,000 computers worldwide. The user downloads and installs the BOINC client on the computer and then attaches to any of a number of very worthwhile projects at august institutions and universities around the globe. Work Units (WU’s) are dispatched to the computer from the projects. The computers “crunch” the data and send the results back to the mother ship. So, we who participate are called “crunchers“. With about one billion computers in the world, you can see that we are a very small community. But, most of us are very committed to this work. We would like to be a much larger community. You could help by joining us.

Here is how Rosetta is described at its web site:

“Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s (See our Disease Related Research for more information). Please join us in our efforts! Rosetta@home is not for profit.”

Rosetta@home is based at the University of Washington, “U-Dub”, in the Baker Laboratory. Dr. David Baker is the Principal Investigator.

You can follow Rosetta@home at Twitter, @rossettaathome

The software built by Rosetta is used in other projects, such as the Human Proteome Folding (HPF2) project which is under the aegis of World Community Grid
Dr. David Baker is a Research Participant at HPF2.

So, to the paper. I am going to only provide enough material to entice the reader to the whole paper.

Alternate States of Proteins Revealed by Detailed Energy Landscape Mapping

“After about 2 years of work, millions of CPU hours donated by volunteers from around the globe on Rosetta@HOME and a fruitful collaboration with Daniel Keedy and Jane and David Richardson at Duke University our paper on energy landscapes is finally out! Thank you to everyone who helped and especially to Daniel Keedy @ Duke and all who have donated computing time!”

Michael D. Tyka†, Daniel A. Keedy†, Ingemar André, Frank DiMaio, Yifan Song, David C. Richardson, Jane S. Richardson and David Baker
†contributed equally

“What conformations do protein molecules populate in solution? Crystallography provides a high-resolution description of protein structure in the crystal environment, while NMR [Nuclear magnetic resonance] describes structure in solution but using less data. NMR structures display more variability, but is this because crystal contacts are absent or because of fewer data constraints? Here we report unexpected insight into this issue obtained through analysis of detailed protein energy landscapes generated by large-scale, native-enhanced sampling of conformational space with Rosetta@home for 111 protein domains.”

Interested? You should be. Proteins and protein folding are at the height of importance for biological and computational investigation into diseases which threaten life.

Read the full article here.