| Project Information | Project % Complete | Major Supported Platforms | |
|---|---|---|---|
| Life Sciences | |||
Parabon Computation has research projects
(and will have commercial projects) and has a secure Java client like Popular
Power's. Version 1.4 is available for Windows 9X/2K/NT as of October,
2002. Version 1.3 for Linux is available as of April 24, 2001. You can
download the full client
here. The
client automatically upgrades itself, so you don't need to download updates.
You can
sign up to receive email notification when the Mac and Unix clients are
available.
The client currently participates in one or more of the following projects: an exhaustive regression analysis to identify the specific factors that ease the suffering of chemotherapy recipients, a gene expression analysis and a study of the molecular dynamics of protein folding to create greater understanding of the behavior of cancer cells and how they interact with potential new treatments, and an exhaustive regression analysis of clinical trial data for Amarillo Biosciences, Inc. for a treatment of fibromyalgia syndrome. |
ongoing |
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Participate in health, science, and Internet-related research projects at
grid.org, "a single destination site for
large-scale research projects powered by the
United Devices Global MetaProcessor."
grid.org's first current project is searching for cancer-fighting drugs in partnership with the National Foundation for Cancer Research (NFCR) Centre for Drug Discovery in the Department of Chemistry at the University of Oxford, England. The first phase of this project, THINK, began in March, 2001 and completed in June, 2002. This phase used over 200,000 hours of CPU time to screen 3.5 billion molecules against a range of cancer protein targets. The second phase, LigandFit, began in June, 2002. This phase will further refine the results from the first phase. Oxford has a detailed website about the science behind the project. grid.org also has the latest news about the project and its results. On December 7, 2002, a CDK-2 (Human Cyclin Dependent Kinase 2) protein, 1AQ1, was placed into production for the LigandFit phase. On January 21, 2003, the 821P protein was placed into production. The protein has 30 ligands per work unit and its work units expire after 20.8 days. On February 12, the C-ABL Tyrosine Kinase (1iep) protein was placed into production. The protein has 80 molecules per workunit and its work units expire after 2 weeks CPU time/3 weeks wall-clock time. On February 25, 2003, the 1C1Y protein was placed into production. The protein has 27 ligands per work unit and its work units expire after 3 weeks. On March 10, 2003, the Farnesyltransferase (1D8D) protein was placed into production. The protein has 30 ligands per work unit and its work units expire after 3 weeks. Note that this is a large protein, with about a 574 KB download and with no protein graphic in the client. On April 19, 2003, a Smallpox protein named "Model 1" was placed into production. It has 220 ligands per work unit and its work units expire after 3 weeks. On July 15, 2003, the final Smallpox protein, named "Model 10," was placed into production. It has 110 ligands per work unit and it work units expire after 3 weeks. grid.org's second current project was searching for a cure for Smallpox in partnership with "Accelrys, Evotec OAI, IBM, Oxford University, United Devices, and numerous scientific researchers led by Dr. Grant McFadden and Dr. Stewart Shuman." This project began on February 5, 2003 and ended on September 30, 2003. It screened "approximately 35 million molecules against a series of protein targets related to Smallpox." Results from the project were submitted to the United States Department of Defense on Septemeber 30, 2003 (see news about this). In the near future, grid.org will continue Smallpox research with a new, modified protein. See the organization's past projects. Version 3.0 of the MetaProcessor client is available as of June 18, 2002. The client will not run on Win95, but will run on all later Windows platforms. Win95 users may wish to run a similar project, such as Distributed Folding or Find-a-Drug. Note for 3.0 users: there is a known bug which causes the client to start from the beginning of a work-unit if you restart the client. Join a discussion group about this project. |
ongoing: 219,823,149 results |
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Folding@home
is another volunteer project that uses a screensaver or client application
based on the Mithral
CS-SDK
to simulate protein folding in an effort to better understand how proteins
self-assemble or fold. Intel supports
this project through its Philanthropic
Peer-to-Peer Program. You can see what projects are currently running
on the current projects
page. As of version 3.0, the software client also supports the
Genome@Home project.
See the project's latest news (last updated October 1, 2003).
On October 21, 2002, the project announced that it achieved its initial goal: to "simulate the folding dynamics of proteins and make quantitative predictions for how [protein folding] works. This has been a 'holy grail' of computational biology." Specifically, the project simulated the folding of a man-made chain of 23 amino acids called BBA5. The simulation's measurements and folding-time matched physical measurements and folding-time of the protein observed in a lab. The achievement was published in the November, 2002, edition of Nature, in an article titled "Absolute comparison of simulated and experimental protein-folding dynamics." On January 10, 2003, the project broke the 90,000 active CPU mark. On October 10, 2003, it broke the 120,000 active CPU mark. On November 28, 2001, the project began studies (110 and 5100) on Alzheimer's Disease. On May 8, 2002, the project began studies (503 and 504) on Huntington's Disease, a disease similar to Alzheimer's Disease in that it is caused by protein misfolding. See a list of all of the project's current studies. In June, 2002, the project started using the Gromacs molecular dynamics modeling software. This software allows the project to simulate larger proteins more accurately and much more quickly than the previous software. As of August 12, 2002, the Gromacs software has successfully modeled one of the simpler molecules, project 902, and shows a lot of promise for success with larger molecules. On March 27, 2003, the project began studying several new types or work units, including NTL9 (a protein with both beta and alpha structure) and 1PRB (a three-helix bundle). The project also increased the scope of its trpzip investigation to include a fourth variant trpzip4. Version 3.24 of the Windows, Linux and Mac OS X clients is available as of December 31, 2002. Note the 2.x clients have a compatibility problem, and you should upgrade to the latest client if you are using an old version. Version 1.34 is available for Solaris (2.7 or higher) at the old project site as of February 25, 2001. See the research papers and articles published from the results of this project. See a Japanese translation of this site. See independently-maintained hourly team and user stats for this project at statsman.org. See an independent support site for helpful hints about participating in this project. See the original Folding@Home project. Join a discussion group about this project. Join a discussion group about the original project. Join an independent discussion group about ab-initio protein folding (where the folding is simulated completely in software) |
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Help design new drugs to fight
AIDS at
fightAIDS@home. The project is sponsored by the non-profit
Scripps Research Institute. The
project completed Phase I on May 21, 2003 (in this phase, almost 60,000
computers completed 1,400 years of computing to process over 9 million tasks).
"[Phase I] has ably demonstrated that with such massive computational abilities, researchers can utilize intensive approaches to identify drug candidates that succumb to resistance mutations and those that are more resilient to such mutations. An early lead developed during Phase I, TL-3, has been shown to be promising against the drug resistant strains that have arisen from the currently approved HIV Protease inhibitors. The characteristics of TL-3 have been born out by the FAAH computational work." The project began Phase II on May 21, 2003. Note that for Phase II, the project transfered completely to The Scripps Research Institute (and became a completely non-profit project) and Entropia is no longer involved. You will need to reregister and download a new client to participate in Phase II. The client is currently available for Windows. It is best for users with permanent Internet connections. The client will eventually be available for Mac OS X and Linux. |
waiting for Phase II stats to become available |
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Übero's Java-based
client allows you to participate in for-pay projects
similar to other current and upcoming for-pay projects. The current Beta
version of the client runs "genetic alignment algorithms" which "look for
similar amino acid strings in various organisms." This volunteer project
is being done for the Institute of Genomics
and Bioinformatics at the University of
California, Irvine. Future volunteer projects may include protein
folding and radiation research. Note: this project
was completed in November, 2001, so no new results are being discovered.
However, the project data is being used to test new features for the client
application. Your contribution will help to test the new features and
improve the client.
The Beta version 0.7.1 of the client is available as of January 8, 2002. This version of the client has support for users behind proxy-based firewalls, uses your CPU and network bandwidth more efficiently, and has many other new features. The client will run on any platform that will run Java 2. This project is better suited for users with full-time Internet connections because a work unit completes in only a few minutes on my Pentium II 350 and the client doesn't buffer work units. View the project's discussion forum. |
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Help find oral drugs which can fight
Anthrax,
Smallpox,
Ebola,
SARS, deadly diseases for
which there is currently no cure, and
Malaria, a life-threatenting
disease for which 40% of the world's population is at risk, in
the
Drug Design Optimization
Lab (D2OL)TM. This
project, sponsored by The Rothberg
Institute for childhood diseases, uses volunteer resources to screen
Anthrax, Smallpox, Ebola, SARS, and Malaria proteins against a database of
2 million potential drugs. The SARS project began on April 17, 2003. The
Malaria project began on November 7, 2003. See a
detailed discussion about the
science behind the project.
The graphical client can run minimized or (on Windows) in the system tray. Currently it does not allow you to select which protein target(s) to work on: future versions will allow this. It does not require a continuous Internet connection: it allows you to set the number of work units it will cache so that you can cache more work if you connect to the Internet infrequently. Note that if you pause or restart the client, you will lose all of the conformers you've generated for the current work unit. The client supports users behind firewalls. Version 2.0 of the client is available for Windows, Mac OS X, Linux and Solaris as of September 18, 2003. See a press release about the significant updates in this version. Join the D2OL discussion forum. |
ongoing: 1,124,277,376 conformers tested; 15,908,240 candidates generated; Anthrax Lethal Factor: 38.217% complete; Smallpox Target 1: 37.412% complete; Ebola Target 1: 37.778% complete; SARS Target 1 / 2 / 3 / 4: 72.257% / 38.038% / 35.208% / 37.962% complete |
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Help screen molecules to design drugs to fight diseases
in The Virtual
Laboratory Project. This project does not work in the way that traditional
projects do. Instead of downloading a software client and
having it get work assignments, you set up Globus
grid computing software on your system and then
make your
system available to the World Wide Grid (WWG), a global computing grid.
Then the Virtual Lab project coordinators can schedule computations on your
system at their convenience. Because of this setup, this project is best for
users with permanent Internet connections. For this project, the
coordinators use their grid scheduler, called Nimrod-G, to deploy their
Nimrod-G agents on your machine to do the molecule screening. Their view of
the project looks like
this.
See a white paper about this process: The Virtual Laboratory: Enabling Molecular Modeling, and a PhD thesis. The biology collaborator working on this project has already designed a drug to counteract an ECE enzyme involved in heart stroke, and is currently using the Virtual Laboratory to study liver cancer. See another white paper by the project coordinators: Grids and Grid Technologies for Wide-Area Distributed Computing. Note: this project is currently only for Linux/Unix users. Windows is not supported yet. |
ongoing |
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Fold proteins to help scientists learn how proteins
"fold and assemble into living cells" in
Distributed Folding. The
project, run by the Samuel Lunenfeld
Research Institute, the
Hogue Bioinformatics Laboratory and the
University of Toronto
Department of Biochemistry, and supported by
Intel's
Philanthropic Peer-to-Peer Program,
is testing a protein folding algorithm to see if it can reproduce natural
protein folds. The project hopes to create "the largest samples of protein
folds ever computed." In its first phase, 1a, it made 1 billion folds for five
small proteins. In phase 1b it made 10 billion folds for 10 large proteins.
Phase 2 began on June 17, 2003. Eventually it will make 100 billion folds
spanning 15 different proteins.
Between May 30, 2002 and September 9, 2002, the project competed in the CASP5 structure prediction contest. Results of the competition were made available in late December, 2002. The project received a patent (U.S. Patent number 6490532) for its structure generation algorithm on December 3, 2002. See the results of the proteins which have been completed for this project. The application runs as a screensaver on Win32 and as a text client on Win32, Linux, Sony PlayStation 2 Linux, and many Unix platforms including Mac OS X. The client folds protein structures and reports its results to the project server every few thousand structures (after several hours) or when you exit it. If the client can't connect to the server, it will buffer the results and try again later (it can be set up with unlimited buffering so that you can connect when you want to). The Windows screensaver version has an option for modem users to tell it not connect to the Internet. The client also detects software updates and automatically updates itself (after it notifies you and you approve the update). Users with a lot of machines can download an auto-update proxy daemon to make it easier and faster to update the client software on all of their machines. The client supports users behind firewalls if they can use non-authenticated proxy servers. The latest version of the client and screensaver is available for all platforms as of October 28, 2003. The latest version of the auto-update proxy daemon is available as of September 2, 2003. View a Windows Media Player ASF-format file of a television interview by CityPulse24 of the project coordinators on November 27, 2002. Join a discussion forum about this project.
CASP5 target results: |
phase 2: v127: 100.0%, best RMSD: 4.84 (August 13, 2003) G: 100.0%, best RMSD: 2.54 (September 3, 2003) L: 155.2%, best RMSD: 3.58 (October 3, 2003) L (variation): 107.8%, best RMSD: 2.75 (October 28, 2003) 1YCC: 58.2%, best RMSD: 8.80
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Join the
CommunityTSC
project and
help find drugs to fight Tuberous Sclerosis
Complex (TSC), "a genetic disorder that leads to benign tumors in
multiple organs, including the brain, kidneys, heart, eyes, lungs and other
organs. The project is sponsored by
The Rothberg Institute
for childhood diseases. The project began work on its second protein
target, PI3K, on June 17, 2002. The project began working on revised
PTEN and PI3K protein targets and new FRAP and EIF4E targets in February, 2003.
The project began working on the AKT protein target on November 3, 2003.
The project uses the D2OL software client. On Windows the client runs in the system tray, but in all versions it also has a graphical interface and a command-line interface to allow you to watch what it's doing. It does not require a continuous Internet connection: it allows you to set the number of work units it will cache so that you can cache more work if you connect to the Internet infrequently. Note that if you pause or restart the client, you will lose all of the conformers you've generated for the current work unit. The client supports users behind firewalls. Version 2.0 of the client is available for Windows, Mac OS X, Linux and Solaris as of September 18, 2003 (see a press release about the significant updates in this version). Join the TSC discussion forum. |
ongoing: 436,447,586 conformers tested; 21,460,900 candidates generated; PTEN 48.773%; P13K 54.164% EIF4E 49.845% FRAP 54.392% |
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Help researchers find new drugs for major diseases at
Find-a-Drug, a non-profit project
run by Treweren Consultants, creators
of the THINK screensaver. Find-a-Drug runs one or more
projects, although
some projects may not be active at any given time.
Project newsletter #4 was
published July 9, 2003.
On June 30, 2003, the project announced that it successfully found some potential cancer-inhibiting drugs. After testing over 500 million molecules, it produced a set of candidates. 39 candidates were tested in a laboratory, and 7 of those (20%) showed the desired anti-cancer properties. Only 2-3% were expected to show the desired properties. On November 12, 2003, the project announced that it has found growth inhibitors for 5 anti-cancer protein targets. "42 of the 200 molecules tested [so far] showed the desired anti-cancer properties." The Cancer and Proteome projects are active as of August 8, 2002. The Bioterrorism Antidotes project is active as of October 15, 2002. A new methodology project is active as of October 26, 2002 (methodology projects improve the performance and accuracy of the Think software). A new protein, Tyrosine phosphatase (PTP1B) was added to the methodology project on February 19, 2003. The Respiratory Disease (starting with SARS) and Multiple Sclerosis projects are active as of May 7, 2003. A second SARS target was begun on May 29, 2003. The HIV project is active as of July 1, 2003. The client supports users behind firewalls. It allows you to easily opt in and out of any of the drug-finding projects, so you can participate in only the projects that interest you. And it allows you to buffer work units so that you can work off-line. Version 1.21l of the client is available for Windows and Linux as of June 11, 2003. Join a discussion forum about the project. |
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