About Folding@home

Pande lab Stanford University

The Pande lab is the founding scientific group of Folding@home. The lab is part of the Departments of Chemistry and of Structural Biology, Stanford University and Stanford University Medical Center, and works on theory and simulations of how proteins, RNA, and nanoscale synthetic polymers fold. We have founded the project, developed methods for using distributed computing to study long timescale dynamics, pushed 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 on our web page.

Affiliated labs

Running and further enhancing FAH is quite involved these days. We've come a long way from the days were it was mainly me and just 2-3 other people. Right now, there are about 20 people in the Pande lab who all are involved in one way or another, but even that isn't enough to make progress in certain key areas. To help with that, we have started to collaborate with other labs.

Chong lab, University of Pittsburgh

The Chong group uses simulation to study many aspects of proteins, in particular unstructured proteins and the behavior of p53, a tumor supressor relevant for cancer (indeed roughly half of all cancers involve some mutant of p53). The Chong group is helping out with new AMBER core development in Folding@home.

Dill lab, UCSF

Ken Dill and his lab has been a pioneer in studying protein folding and other biomolecular questions. We are collaborating with members of his group on free energy calculations and structure prediction.

Izaguirre Lab, Notre Dame

The Izaguirre lab is interested in problems at the interface between biology, computer science, and applied mathematics. Their lab has developed the Protomol MD package, and we are working together to integrate that package into Folding@home. Protomol is a great package for testing and developing new algorithms and will likely be useful for FAH in the future.

Shirts lab, University of Virginia

Michael Shirts's group at the University of Virginia develops new simulation methodology and uses simulations to predict thermodynamic properties for small molecules. They are collaborating with us to develop new versions of the Gromacs core and general Gromacs core development.

Sorin lab, CSULB

Eric Sorin's group at CSULB uses simulation to study protein folding and other related areas. They are collaborating with us to develop new force field ports for Gromacs.

Zagrovic lab, Mediterranean Institute for Life Sciences

Bojan Zagrovic's lab at the Mediterranean Institute for Life Sciences in Croatia is interested in many related areas, including unstructured proteins and experimental structure refinement. His group is helping out Folding@home with new client development.

Community volunteers

A great deal of the support for the Folding@home software comes from volunteers in the Folding@home community. There are many different ways that people have helped. Countless numbers of people have helped by answering each others questions on the Forum and there are too many to cite completely here. Nevertheless, we have listed a few who have made particularly major contributions.

Moderators

We are grateful for all the work the Folding Community Forum (FCF) moderators have done to keep the FCF running smoothly and to directly help donors run Folding@home -- we are grateful to them all. Moreover, the are several moderators at the forum who also have helped us beyond the forum, including beta testing and even help with these web pages. Of particular note are Bruce Borden's (Bruce) contributions in general, Wiebo Westerhoff's (WW) hosting of the forum, and Tim Braun's (7im) great efforts to improve the FAH web pages.

Translators

We must also thank the numerous translators who have worked on translating the Folding@home web pages into many other languages.

FAQ and Guide team

We're indebted to the team of volunteers who help us keep to date FAQ and documentations. This includes Stephane Renaud (Xilikon) for his help with and creation of the Guides and 7im's and Ivoshiee's help with the FAQ.

Developers

We are also working with community software developers. These developers have been working to help us improve our software as well as to make better interfaces for 3rd party utilities. We would like to especially thank Andrew "Uncle Fungus" Schofield for his contributions to the project.

Commercial partners

We work closely with companies in many of our projects. In particular, we have collaborated with commercial partners in the development of our client, core, and backend server software.

Intel (2001-2002)

One of our earliest partners was Intel, who helped fund part of Folding@home through it's Philanthropic Peer-to-peer Program.

Google (2001-2003)

Google participated in Folding@home via it's Google Compute client for FAH. Google compute was built into the Google toolbar, thus making it very easy for people to run Folding@home -- no installation, just say "yes" when asked.

Sony (2005-present)

We have been collaborating with Sony on the Folding@home software for the PS3. This included all the components largely fron scratch, especially optimizing the scientific code to run efficiently on a PS3. The result was a really beautiful client with great performance.

ATI (2005-present)

We've been working with ATI for quite a while on our GPU core. This started with GPU1 and has carried over to GPU2.

NVIDIA (2007-present)

We've been working with NVIDIA on the GPU2 port for NVIDIA hardware. In a collaboration between NVIDIA personnel (Scott LeGrand) the Folding@home team, we have ported and optimized our code to CUDA.

Cauldron Development (2007-present)

We have been working with Cauldron Development (http://www.cauldrondevelopment.com/) to rewrite the FAH server code from scratch. This should make our code much more reliable and easier to extend. This is the software foundation for the next 10 years of the Folding@home project.

Funding and support

There are several organizations which fund our work:

Most notably, a large bulk of our funding comes from the United States' National Institutes of Health (NIH) and National Science Foundation (NSF). We also thank (in alphabetical order) Apple, ATI, Dell, Google, Intel, and Sony for their support over the years. Finally, we have been supported by NIH Roadmap centers Simbios and the Protein Folding Nanomedicine Center.

More specifically, 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. The GPU and PS3 work has been in part supported by Simbios (supported by the National Institutes of Health through the NIH Roadmap for Medical Research Grant U54 GM072970).

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.

Miscellaneous

Cosm

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.

TINKER

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.

Gromacs

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.

About the Logo

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:

We would like to thank Mark Lowe and Rob Goodlatte for all their help with the logo and web redesign. We would also like to thank Po' Smedley for his icon design.

About the screen saver

Our screen saver shows real time visualizations of the simulations being performed. The molecule drawn is the current atomic configuration ("fold") of the protein being simulated on your computer and the pie chart the left shows the current progress on the work unit.

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.

Last Updated on August 22, 2008, at 12:22 PM