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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 clients 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: the Folding@home Consortium (FAHC)

Running and further enhancing FAH is quite involved these days. We've come a long way from the early days in 2000 where it was mainly Prof. Pande and just 2-3 other people. Right now, there are about 20 people in the Pande lab who are involved in one way or another. But even that isn't enough to make progress in certain key areas. To help, we have started collaborating with other labs to form a consortium of labs involved with running, improving, and applying Folding@home to do even greater research than we've done before.

Huang Lab, HKUST

Xuhui Huang's lab at HKUST is interested in conformational change, which is crucial for a wide range of biological processes including biomolecular folding and the operation of key cellular machinery.

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 have integrated that package into Folding@home. Protomol is a great package for testing and developing new algorithms. Particularly, Protomol implements the Normal Mode Langevin method for doing Long Timestep Molecular Dynamics (LTMD). This allows timesteps hundreds to thousands of times longer than conventional molecular dynamics. We are running Folding@home projects using LTMD to explore the effect of mutations on protein folding. Future projects will explore the effects of conformational dynamics in function and protein aggregation. Also, in the future, LTMD will be fully incorporated into OpenMM to benefit from hundred-fold speedups from GPU acceleration.

Kasson Lab, University of Virginia

Peter Kasson's lab at U. Va works on lipid membrane biophysics, especially as it has a role in viral infection. Dr. Kasson has worked extensively on the SMP core for Folding@home.

Lindahl Lab, Stockholm University

Erik Lindahl's group is well known as a primary developer of Gromacs, a powerful MD code that is frequently used in Folding@home. He also has interests in lipid membrane biophysics and viral fusion, leading to many collaborations on that front as well.

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.

Snow lab, Colorado State University

The Snow lab at Colorado State has developed a new scientific core to run SHARPEN on Folding@home. These upcoming projects will test the performance of new algorithms for high-resolution protein structure prediction and also for the design of libraries of enzymes.

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.

Voelz lab, Temple University

Vincent Voelz's lab at Temple University's Chemistry Department focuses on using transferrable, all-atom simulations for prediction and design of biomolecular dynamics and function. In particular, their interests include in silico prediction and design of proteins, peptide mimetics (e.g. peptoids), and binding sequences for cell signaling peptides.

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 Folding 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 Forum moderators have done to keep the forum 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 up to date the FAQ and documentations. This includes Stephane Renaud (Xilikon) for his help with creating the install Guides pages, 7im's help maintaining 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.

Stonehopper (2011-present)

We've gotten design help from Stonehopper (http://stonehopper.com/) in our web page revamping that was released in 2012.

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.

Software used in Folding@home

OpenMM

The GPU core for Folding@home extensively uses the OpenMM MD package.

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.

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.

Last Updated on August 02, 2012, at 11:02 AM