| 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
United Devices.
United Devices' 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. United Devices 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 product for the LigandFit phase. United Devices is also running its first commercial project, web performance testing, in partnership with Exodus Communications. User participation in this project is optional, but your work will help United Devices stay in business and run more voluntary projects. See the company'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: 172,983,654 results |
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Folderol is a volunteer project that
uses a screensaver, command-line client or system client application to
simulate protein
folding of the data from the Human
Genome Project.
Version 0.62 is available as of June 17, 2001. September 27, 2001 Note: The project coordinators have stated that this project is on hold indefinitely, until they have time to support it again. They will let us know when it resumes. For now, please try a different project. |
on hold; 36 years of simulations completed. |
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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 21, 2002).
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 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. Version 3.14 of the Windows and Linux clients and version 3.12 of the Mac OSX clients is currently available. 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 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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ongoing |
 
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Help design new proteins and genes for
Genome@home, a sister project
to Folding@home, to learn better how natural genomes have evolved and how
natural genes and proteins work. See the project's
latest news (last updated
September 5, 2002).
Genome@home's first experiment concluded successfully in early March, 2001, with more than 1000 users creating more than 15,000 new genes for 217 proteins. As of November 12, 2001, Genome@home has begun Phase 2 of its protein design experiments. This phase will study "all single-chain proteins in the RCSB Protein Data Bank" with a length up to 150 amino acids--over 3,015 different proteins. On May 1, 2002, Genome@Home began a new series of RMSD (root-mean-square deviation) projects to study the structural diversity of "ensembles of protein backbones" used in the design of large proteins. The following paper has been published from the results of this project:
This project is supported by the Folding@Home version 3.0 client software. For now you can also use version 0.99 of the Genome@Home client, available as of August 2, 2001. A work unit takes 24-48 hours to complete, but the software now has checkpointing so that you can restart work unit if you have to stop it before it finishes. For modem users with version 0.99, the client will continue designing new genes for the last work unit you downloaded until you reconnect to the server, and then it will upload your results and download a new work unit to work on. See independently-maintained hourly team and user stats for this project at statsman.org. Join a discussion group about this project. |
ongoing |
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Help design new drugs to fight
AIDS at fightAIDS@home using
the entropia client.
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ongoing: 8,092,503 tasks done |
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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. |
ongoing |
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Help find an oral drug which can fight
Anthrax,
Smallpox,
and Ebola, deadly diseases for
which there is currently no cure, in
the
Drug Design Optimization
Lab (D2OL)TM. This
project uses volunteer resources to screen the Anthrax, Smallpox, and
Ebola proteins against a database of 2 million potential drugs.
Version 1.0 of the client is available for Windows, Mac OS X, Linux and Solaris as of July 4, 2002. On Windows it 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. Note on an important bug fix for version 1.0 for Windows users only: a bug that has caused recent project server issues and that has caused client software for some users to open many connections to the project server has been fixed. But the fix cannot be downloaded automatically. You can download a new installer from the downloads page or find more information about the fix file and how to install it on the discussion boards. Note for Solaris users: the client requires the following libraries from
gcc 3.1: libstdc++.so.4, libgcc_s.so.1. If these libraries are not installed
on your system, you can download the libgcc 3.1 package from
sunfreeware.com (the package expands
to about 225 MB) or download these specific files from aspenleaf using
the following links:
Join the D2OL discussion forum. |
ongoing: 103,133,908 conformers tested; 5,158,933 candidates generated; Anthrax: 17.97% complete; Smallpox: 15.28% complete; Ebola: 26.59% 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, it made 1 billion folds for five
small proteins (phase 1a). In phase 1b it is making 10 billion folds for 10
large proteins (phase 1b). 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 will be known in late December, 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, 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 is available for all platforms as of December 10, 2002. Note that a new algorithm in this update causes the error.log log file to grow quickly. The next update will include a fix to prevent the log file from growing larger than 1 MB. You can download the fixed client from the website now, or delete error.log to fix the problem temporarily. 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 1a: 1ENH: 100%, best RMSD: 3.64 (March 15, 2002) 1PMC: 100%, best RMSD: 3.96 (March 23, 2002) 5PTI: 100%, best RMSD: 5.40 (April 1, 2002) 1VII: 100%, best RMSD: 2.19 (April 8, 2002) 1SHG: 100%, best RMSD: 6.52 (April 15, 2002)
phase 1b:
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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 will begin working on revised
PTEN and PI3K protein targets and new FRAP and EIF4E targets in early 2003.
The project uses the Sengent 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. The latest version of the client is available for Windows, Mac OS X, Linux and Solaris as of October 24, 2002. This version allows the project coordinators to "modify some of the docking parameters on the fly, enabling [them] to tweak the system to improve its performance and accuracy." Note for Solaris users: the client requires the following libraries from
gcc 3.1: libstdc++.so.4, libgcc_s.so.1. If these libraries are not installed
on your system, you can download the libgcc 3.1 package from
sunfreeware.com (the package expands
to about 225 MB) or download these specific files from aspenleaf using
the following links:
Join the TSC discussion forum. |
ongoing: 119,749,529 conformers tested; 5,990,891 candidates generated; PTEN protein 25.594% complete; PI3K protein 5.006% complete |
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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 #2 was
published September 13, 2002.
Version 1.20j of the client is available as of December 10, 2002. The client is currently only available for Windows. It 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. 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). Join a discussion forum about the project. |
ongoing |
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