Drug Design and Optimization Lab

This project is hosted at The Rothberg Institute for Childhood Diseases in the huge city of Guilford, CT. Check out some glamour shots of the crew here. Their software agent that you can download will use your computer to help researchers narrow down the field of potential drug candidates to combat Anthrax, Smallpox, Ebola, SARS and other diseases.

evolution@home

Evolution@home simulates certain types of evolution with a semi-automated program where you have to e-mail the results back to the project yourself. The current phase is attempting to answer questions about species extinction. We all know what the theory of evolution is, but here is a funny quote from the website, "As most people know, deleterious mutations happen more often than advantageous ones." Do you really think so!? This project has been ported to BOINC Platform using the BOINC wrapper application.

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Folding@Home

This is one of the older protein simulation projects, and one of the few that does not use the BOINC Platform. It started on October 1st, 2000. If you want to see pictures and movies of proteins that have been simulated in the past, check them out here. The team has published 45 papers at last count.

The Folding@Home team began by simulating proteins such as an alpha helix, then HIV and a beta-beta-alpha fold and the villin headpiece. The predicted folding times for these proteins were quite close to the actual folding times for the molecules. After testing these results, the team knew that their simulation algorithm was on the right track. The team has proceeded to computational drug research, studies on cancerous tumor suppressors, and work on the folding of proteins and peptides in confined spaces.

Their current and completed projects deal with:

• Alzheimer's Disease
• Cancer
• Huntington's Disease
• Osteogenesis Imperfecta
• Parkinson's Disease
• Ribosome & antibiotics

MalariaControl.net

MalariaControl.net is an effort to predict the spread of malaria in Africa. These predictions are formulated by taking many biological and social factors into account. The results from the calculations will help scientists know where to deploy malaria fighting tools such as vaccines, mosquito nets, and chemotherapy.

Predictor@Home

Using VC to test and evaluate new algorithms and methods of protein structure prediction. Why? The connection between protein structure and protein sequence is helpful for scientist to know especially with the unraveling of the human genome. You should probably go here to read their own explanation because I have watered it down substantially. Check out the crew's photo shoot here. Pay close attention to Professor Charles L. Brooks III as he stares at a fly on his office wall. This project uses the BOINC Platform.

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Rosetta@Home

Rosetta@Home uses the BOINC Platform to predict the 3-d shapes of proteins. Why? This research will help our understanding of diseases such as HIV, Malaria, Cancer, and Ithcy-Itchy-Bang-Bang. There is a great explanation of how this process works here, one of the best explanations of protein folding on the net. The project does a great job of communicating with participants with frequent news updates, a clear and easy-to-understand website, and RSS feeds for those who like their information served in style.

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SIMAP

SIMAP has a database of about all currently published protein similarities and protein domains. Public databases have accumulated a massive number of protein sequences and these data are constantly being updated. This creates a need for the power the FASTA algorithim to continue searching for similarities. SIMAP uses the BOINC Platform.

World Community Grid

IBM and United Devices have teamed up to "tackle projects that benefit humanity." They have pledged to work with only public and not-for-profit organizations and to place all results in the public domain available to the research community. The Linux option uses the BOINC Platform.

Below are the current projects for this platform.

1. AfricanClimate@Home. The African continent is more vulnerable to severe weather because of its lack of infrastructure to deliver fresh water, irrigation, health care, and other facilities. Because of this vulnerability, scientists are developing this new system of climate prediction to gain a more accurate understanding of the local climates and how they may change with global warming. Current climate models offer a resolution of only 300km which is not sensitive enough to account for the effect of changes in specific regions. AfricanClimate@Home is using distributed computing to reduce the resolution to 30km which should provide a more accurate picture for predicting future climate change in the region.
2. Discovering Dengue Drugs – Together. Dengue, Hepatitis C, West Nile, and Yellow Fever virus affect millions of people throughout the world. There are currently no drugs for effectively combating these illnesses. The goal of this project is to find drug candidates that inhibit the viral NS3 protease through the use of computational chemistry. The NS3 protease is needed for these viruses to replicate. The University of Texas Medical branch is running this project and it is expected to be completed by the end of 2008.
3. FightAIDS@Home. According to UNAIDS, a United Nations program, there were an estimated 40 million people living with AIDS in 2006 . No cure has been found. HIV mutates in form which makes finding a cure even harder. FightAIDS@Home is using World Community Grid's large volunteer base to get users for its Autodock software. Autodock runs protein simulations to finds new drugs the could be used in the treatment of AIDS.
4. Help Conquer Cancer. The structure of a protein after it is folded reveals many important aspects of that protein including how it interacts with other proteins. The Help Conquer Cancer project is using X-Ray Crystallography, instead of simulated folding, to determine unknown protein structures. X-Ray Crystallography is a complicated procedure in which x-rays are sent through crystallized proteins to predict their structure. In order for this to work correctly, the target protein must be correctly crystallized. To get a well-formed crystal, the experiment needs to be performed many times on each protein while altering several different conditions. The computer power of WCG comes into play to analyze 86 million images from 9400 proteins to see which images contain well formed crystals. The well-formed crystals can then be used to determine the structure of the protein. Also, by figuring out which conditions created good crystals, X-Ray Crystallography techniques can be improved.
5. Human Proteome Folding project Phase 2. The main objectives of this stage are investigating higher resolution protein structures and improving the Rosetta software.

• Help Defeat Cancer project. Completed April 2007. Unlike most of the other bioscience projects, Help Defeat Cancer is not simulating pharmacuticals or protein folding. This project is comparing Tissue Microarrays of different types of cancer. Comparing the tissues makes it possible for researchers to determine the specific type and stage of cancer.
• Genome Comparison Project. Completed July 2007. As scientists study genes and discover new information, they put it into one of many different databases. As more information is discovered, the old information is sometimes not updated properly. Over time, this has resulted in inaccurate information for many gene sequences. This project is attempting to "perform, for the first time, a complete pairwise comparison between all predicted protein sequences" to improve the accuracy of the existing information. The project will use an open and available algorithm and the results will be available for all to see.
• Help Cure Muscular Dystrophy. Phase 1 completed June 2007. No current work. Neuromuscular diseases are a collection of over 200 disorders that impair muscle function through either muscle pathology (called muscular dystrophy) or through nerve pathology. The most well known type of neromuscular disease is muscular dystrophy. There are over 30 types of muscular dystrophy which vary in rate of degeneration, age of onset, and pattern of inheritance. Duchenne MD is the most common form of muscular dsytrophy. It affects mostly boys, comes between the ages of 3 and 5, and the child is unable to walk by the age of 12. More information on muscular dystrophy is available the National Institute of Neurological Disorders and Stroke here. This world community grid project will be helping in the fight against neuromuscular disease by simulating protein to protein interactions for known protein structures including those that are mutated in these diseases. The simulated interactions will give scientists clues that may help them design future treatments for neuromuscular diseases by having a better understanding of the interactions at a molecular level.

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Xgrid@Stanford

This is a research project for Macintosh computers only which has a goal to "modelize the conformational changes of the beta 2 adrenergic receptor". No one knows what this means, but you can read more words like that in the web site's project section. They have a cool looking dashboard widget too, check it out.

APS@Home

APS@home is studying the effect of atmospheric dispersion on measurements used in climate prediction. For example, if a measurement is taken in a specific area to determine CO² absorption of a forest, how does the observer know that the results gathered aren't skewed from gases blowing from an adjacent marsh? This problem will be addressed by simulating the turbulence in the area and sampling the particles that travel to the area where the measurements were taken to discover their origin.

Climateprediction.net

Now greenies can do something for the earth with volunteer computing. Climateprediction.net runs climate projections with different key variables changed such as sulfur and carbon dioxide levels. The different future climates that these simulations are producing are helping scientists study the possibility and severity of global warming. Is global warming real? Put your SUV in park, load this program, and help us find out! This project uses the BOINC Platform.

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Seasonal Attribution

This project is no longer sending out new units. Please see the news link below.

A close relative of Climateprediction.net, this variant is running parallel climate models--half with human-induced climate change, and half without. The point is to see if human-induced climate increases our chance of extreme weather risk.

The extreme weather incident that this project mentions is The UK Autumn 2000 Floods. These floods occurred during the wettest autumn on record in England and Wales in since record keeping started in 1776.

This project uses the BOINC Platform.

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ABC@home

The ABC Conjecture was first conjured in 1985 and its subject matter is connected to many other problems in number theory. ABC@home is an attempt to solve the ABC conjecture.

From the ABC@home website: "The ABC conjecture involves abc-triples: positive integers a,b,c such that a+b=c, a < b < c, a,b,c have no common divisors and c > rad(abc), the so-called radical of abc. The ABC conjecture says that there are only finitely many a,b,c such that log(c)/log(rad(abc)) > h for any real h > 1. The ABC conjecture is currently one of the greatest open problems in mathematics."

distributed.net

Distributed.net is currently running two volunteer computing efforts.

Project OGR - This project searches for Optimal Golomb Rulers. A Golomb Ruler is a set of points upon an imaginary line where no points are the same distance apart and all distances between points are a non-negative integer value. An Optimal Golomb Ruler is the shortest Golomb Ruler for a given number of points.

Optimal Golomb Rulers become exponentially more difficult to discover as the number of points increase. Project OGR is now working on finding a 25-point OGR. One real-world application of an Optimal Golomb Ruler is the design of antennas.

Project RC5-72 - The theory with Project RC5 is - if we try every possibility we will eventually find the right one. Otherwise referred to as a brute force attempt, RC5 is trying to crack the RC5 encryption key by guessing every possibility until the correct code is found. Using this same method, the 56-bit key was found in 250 days and the 64-bit key was found in 1,757 days. The current key is 72-bits.

RC5 is an encryption technology that involves a variable block size of 32, 64 or 128 bits, a number of rounds that ranges from 0 to 255 and a key that can range from 0 to 2040 bits. The first organization to crack this key will be paid $10,000 by RSA. The $10,000 will be divided as shown here.

This project has been ported to BOINC Platform using the BOINC wrapper application.

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The Great Internet Mersenne Prime Search

Impress your neighbor by finding the world's largest known Mersenne Prime. A Mersenne Number is a number that is one less than a power of two (M_n=2ⁿ-1). A Merssene Prime is a Merssene Number that is a prime number. One of The Great Internet Mersenne Prime Search's (GIMPS) recent finds, the 44^th known Mersenne Prime, and the largest of its kind, was 2^32,582,657-1 found on September 4^th, 2006.

Running since January 1996, this is one of the oldest Volunteer Computing projects still in existence today. A $100,000 reward will be given out to the person who finds a prime containing 10,000,000 digits.

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Pi Segment

This is possibly the first politically motivated volunteer computing project. Pi Segment is distributing the calculation of Pi in order to spread the popularity of Volunteer Computing in its home country of China. According to the site, VC has not caught on yet in China so the researcher behind this project wants to change that.

Seventeen or Bust

Volunteer Computing is used in Seventeen or Bust in an attempt to solve the Sierpinski Problem.

From the Seventeen or Bust site: The Sierpinski problem itself deals with numbers of the form N = k * 2^ⁿ + 1, for any odd k and n ≥ 1. Numbers of this form are called Proth numbers. If, for some specific value of k, every possible choice of n results in a composite (non-prime) Proth number N, then that k is called a Sierpinski number. The Sierpinski problem itself is: "What is the smallest Sierpinski number?"

DIMES

This project studies the structure of the Internet by using agent programs written in Java to communicate with their server. Knowing the "shape" of the Internet can help it be used more efficiently. The program does not consume much bandwidth or CPU resources.

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The Lattice Project

The Lattice Project is a multi-purpose grid computing application administered by the University of Maryland. After you attach to the project, several different projects can be run, all from the University of Maryland, such as DNA research, computing Pfam assignments, and statistical analysis.

SoundExpert

Sound Expert aims to estimate perceptual sound quality of various audio devices and technologies (only psychoacoustic coders at the moment though) by means of blind listening tests conducted over the internet. The testing is interactive and controlled entirely by the system. In order to take part in testing visitors are suggested to download a test file (~3Mb), listen it (~15s) and send back a grade. The ratings are computed and visualized in real time while new participants return their grades. The main idea behind the project is consumer control over sound quality measurements of various audio equipment on the market. SoundExpert, being a human distributed project, combines tiny efforts of audio gear users for carrying out this task.

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yoyo@home

Yoyo@home is a combination project. It is using the BOINC wrapper application to enable older applications to run on the BOINC platform without rewriting the old projects from scratch. So far yoyo@home has converted two projects with the BOINC wrapper, they are Distributed.net, evolution@home and Muon1.

• # of active users: 1,200.
• Operating systems supported: Linux, Mac OS X, and Windows.

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