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About Folding@home PANDE GROUP, CHEMISTRY DEPARTMENT, STANFORD UNIVERSITY The Pande group works
on theory and simulations of how proteins, RNA, and nanoscale
synthetic polymers fold. We have developed the
ensemble dynamics method and its application to protein folding
and wrote the client and server code for the Folding@home
project. The members of the group involved with Folding@Home are
listed here. OTHER GROUPS INVOLVED WITH FAH
There are several groups collaborating on Folding@home these days in different ways. Notably:
We would also like to thank the following companies and agencies for their support of Folding@Home. The implicit solvation work (Tinker) is supported by a grant from the National Institutes of Health (R01GM62868-01). Our Gromacs work (i.e. our research on the role of water in protein folding) was recently supported by a grant from the National Science Foundation (NSF). Our work on the comparison between force fields was supported by the ACS PRF (36028-AC4). The education pages were supported by the NSF MRSEC CPIMA (DMR-9808677), which paid for Freedom High School teacher Tug Sezen to spend a summer in our lab developing a Folding@Home-based curriculum and supporting web pages.
We have recently gotten a generous grant in hardware discounts from Dell, which will allow us to revamp our Folding@Home server backend. We would also like to thank Google for their support through the Google Compute program. We also thank Intel for their help in the past through the Intel Philanthropic Peer-to-peer Program. We'd like to thank Apple for their continued support, especially with the development of our OS X client and development of Gromacs for OS X. Finally, we'd like to thank Stanford University for their support of Folding@Home through grants from the Internet 2 program, the Office of Technological Licensing, and an award of a Terman Fellowship to Prof. Pande.
The Cosm project has made significant contributions to Folding@home by developing the network library (Mithral CS-SDK) used to build the client and server code. Adam Beberg is the main force behind Cosm, although there are several people involved in its development.
The protein dynamics part of the Folding@home code is a modified version of TINKER, a powerful molecular dynamics program written by Jay Ponder's lab (in the Dept. of Biochemistry & Molecular Biophysics located at the Washington University School of Medicine in St. Louis, Missouri.). Their continual advancement of their code, including significant speed improvement in the upcoming version, will translate into further advancements in Folding@home. Please see his site for more details. If you would like to "tinker" with his source, please read and sign his license agreement.
We have recently incorporated and heavily modified the Gromacs molecular simulation package for Folding@Home. We are continuing to work with the Gromacs developers to further improve Gromacs. For more details, see our Gromacs page.
Jobs at Folding@home: postdoctoral fellow positions open Interested in simulation and theory of biological molecules? Do you have a PhD in physics, chemistry, structural biology, or a related field? Are you familiar with C, FORTRAN, Perl, HTML, and Linux? If so, we're looking for a few good postdocs to work in the Pande Group (at Stanford University) on Folding@home and related projects. Please email a brief statement or CV to Prof Pande .
Our logo is an abstract representation of our goal: to go from the protein sequence encoded in the genome to the protein's structure. The double helix on the left of the logo denotes the genome (DNA is a double helical molecule) and the arrows on the right are representations of protein structure (beta sheet structure is often drawn as ribbons with arrows).
We've recently updated this look:
Thanks to Mark Lowe for all his help with the logo and web redesign.
There are currently four visualization modes: Space-filling, ball-and-stick, wireframe, and alpha-trace. In ball-and-stick, each small ball represents an atom, and the sticks represent bonds between atoms. In the space-filling model, each filled sphere represents the approximate volume that the electrons occupy around each atom. In wireframe mode, only the bonds are drawn, but with the vertices colored to indicate atom identity. In all but alpha-trace mode, carbon atoms are drawn in dark gray, hydrogen atoms are drawn in light gray (although some hydrogen atoms are not drawn at all), oxygen atoms are drawn in red, nitrogen atoms are drawn in blue, and sulfur atoms are drawn in yellow. In the alpha-trace model, only one atom (the alpha-carbon) is shown per amino acid residue, in order to emphasize the overall arrangement of the peptide or protein. |
