Welcome to PoppaGeek's 

Welcome to the Computing for Clean Water project!

We really appreciate that you are willing to donate your idle computing time to this ambitious project.

Our international team is led by researchers at CNMM, a research centre focused on multidisciplinary aspects of mechanics and based at Tsinghua University in Beijing. With your help, we will be simulating novel filter materials that could help to provide cheap, clean water and even desalinate seawater.

The lack of clean drinking water is a major cause of disease and death in many parts of the developing world these days, and with the rise of global population and the erosion of the environment, this situation is getting rapidly worse. Many steps can be taken by individuals and authorities to reduce water consumption and thereby ease the pressure on demand for clean water. But ultimately, to tackle this problem requires discovering cheaper ways to filter and desalinate water. After all, nearly 97% of the world’s water lies in salty oceans and seas.

One promising route to making such filters is to use arrays of tubular carbon fibres, each only about a millionth of a millimeter in diameter. As initial experiments and simulations suggest, clean water is unusually easy to extract through such filters. Reducing the pressure needed to force water through filters has a direct impact on the cost of any filtration process, and it is this opportunity that our research will seek to optimize. But to understand the optimal conditions for such filtration, we will require millions of simulations under a very wide range of conditions. This is where your computer will play a key role.

We are really looking forward to seeing the results of this project, and sharing the insights we get from it with you. Although what we are doing is quite fundamental science, it can have a significant long-term impact on practical applications, guiding other researchers around the world to develop better filter solutions. As the project moves forward, we will be certain to keep you updated about our findings and publications in this forum. You can also visit the website of CNMM for more information about us: http://cnmm.tsinghua.edu.cn

Official  Announcement and Press Release

Mission
The mission of the Help Fight Childhood Cancer project is to find drugs that can disable three particular proteins associated with neuroblastoma, one of the most frequently occurring solid tumors in children. Identifying these drugs could potentially make the disease much more curable when combined with chemotherapy treatment.

Significance
Neuroblastoma is one of the most common tumors occuring in early childhood and is the most common cause of death in children with solid cancer tumors. If this project is successful, it could dramatically increase the cure rate for neuroblastoma, providing the breakthrough for this disease that has eluded scientists thus far.

Approach

Proteins (molecules which are a bound collection of atoms) are the building blocks of all life processes. They also play an important role in the progress of diseases such as cancer.

Scientists have identified three particular proteins involved with neuroblastoma, which if disabled, could make the disease much more curable by conventional methods such as chemotherapy. This project is performing virtual chemistry experiments between these proteins and each of the three million drug candidates that scientists believe could potentially block the proteins involved. A computer program called AutoDock will test if the shape of the protein and shape of each drug candidate fit together and bond in a suitable way to disable the protein.

This work consists of 9 million virtual chemistry experiments, each of which would take hours to perform on a single computer, totaling over 8,000 years of computer time. World Community Grid is performing these computations in parallel and is thus speeding up the effort dramatically. The project is expected to be completed in two years or less.

What is AIDS?
UNAIDS, the Joint United Nations Program on HIV/AIDS, estimated that in 2004 there were more than 40 million people around the world living with HIV, the Human Immunodeficiency Virus. The virus has affected the lives of men, women and children all over the world. Currently, there is no cure in sight, only treatment with a variety of drugs.

Prof. Arthur J. Olson's laboratory at The Scripps Research Institute (TSRI) is studying computational ways to design new anti-HIV drugs based on molecular structure. It has been demonstrated repeatedly that the function of a molecule — a substance made up of many atoms — is related to its three-dimensional shape. Olson's target is HIV protease ("pro-tee-ace"), a key molecular machine of the virus that when blocked stops the virus from maturing. These blockers, known as "protease inhibitors", are thus a way of avoiding the onset of AIDS and prolonging life. The Olson Laboratory is using computational methods to identify new candidate drugs that have the right shape and chemical characteristics to block HIV protease. This general approach is called "Structure-Based Drug Design", and according to the National Institutes of Health's National Institute of General Medical Sciences, it has already had a dramatic effect on the lives of people living with AIDS.

Even more challenging, HIV is a "sloppy copier," so it is constantly evolving new variants, some of which are resistant to current drugs. It is therefore vital that scientists continue their search for new and better drugs to combat this moving target.

Scientists are able to determine by experiment the shapes of a protein and of a drug separately, but not always for the two together. If scientists knew how a drug molecule fit inside the active site of its target protein, chemists could see how they could design even better drugs that would be more potent than existing drugs.

To address these challenges, World Community Grid's FightAIDS@Home project runs a software program called AutoDock developed in Prof. Olson's laboratory. AutoDock is a suite of tools that predicts how small molecules, such as drug candidates, might bind or "dock" to a receptor of known 3D structure. The very first version of AutoDock was written in the Olson Laboratory in 1990 by Dr. David S. Goodsell, since then, newer versions, developed by Dr. Garrett M. Morris, have been released which add new scientific understanding and strategies to AutoDock, making it computationally more robust, faster, and easier for other scientists to use. From the beginning of this project, World Community Grid has been running a pre-release version of AutoDock4. In August 2007, World Community Grid started running the new publicly available version 4 of AutoDock which is faster, more accurate, can handle flexible target molecules and thus can also be used for protein-protein docking analysis. AutoDock is used in the FightAIDS@Home project on World Community Grid to dock large numbers of different small molecules to HIV protease, so the best molecules can be found computationally, selected and tested in the laboratory for efficacy against the HIV virus. By joining forces together, The Scripps Research Institute, World Community Grid and its growing volunteer force can find better treatments much faster than ever before.

Human Proteome Folding Phase 2 (HPF2) continues where the first phase left off. The two main objectives of the project are to: 1) obtain higher resolution structures for specific human proteins and pathogen proteins and 2) further explore the limits of protein structure prediction by further developing Rosetta software structure prediction. Thus, the project will address two very important parallel imperatives, one biological and one biophysical.

The project, which began at the Institute for Systems Biology and now continues at New York University's Department of Biology and Computer Science, will refine, using the Rosetta software in a mode that accounts for greater atomic detail, the structures resulting from the first phase of the project. The goal of the first phase was to understand protein function. The goal of the second phase is to increase the resolution of the predictions for a select subset of human proteins. Better resolution is important for a number of applications, including but not limited to virtual screening of drug targets with docking procedures and protein design. By running a handful of well-studied proteins on World Community Grid (like proteins from yeast), the second phase also will serve to improve the understanding of the physics of protein structure and advance the state-of-the-art in protein structure prediction. This also will help the Rosetta developers community to further develop the software and the reliability of its predictions.

HPF2 will focus on human-secreted proteins (proteins in the blood and the spaces between cells). These proteins can be important for signaling between cells and are often key markers for diagnosis. These proteins have even ended up being useful as drugs (when synthesized and given by doctors to people lacking the proteins). Examples of human secreted proteins turned into therapeutics are insulin and the human growth hormone. Understanding the function of human secreted proteins may help researchers discover the function of proteins of unknown function in the blood and other interstitial fluids.

The project also will focus on key secreted pathogenic proteins. While still in its early design phases, HPF2 will likely focus on Plasmodium, the pathogenic agent that causes malaria. Researchers hope that higher resolution structure predictions for the proteins that malaria secretes will serve as bioinformatics infrastructure for researchers who are working hard around the world to understand the complex interaction between human hosts and malaria parasites. While there are few silver bullets, and biology is one of the most complicated subjects on earth, researchers believe that this work will help it understand elements of this host-pathogen interaction or at least its components. Researchers will provide their findings as a resource to the scientific community and then work with the community on visualizing, using and refining the data. This understanding could then be a foundation for intervention.

Lastly, this project dovetails with efforts at NYU and ISB to support predictive, preventative and personalized medicine (under the assumption that these secreted proteins will be key elements of this medicine of the future). It is too early to say which proteins will end up being biomarkers (substances sometimes found in an increased amount in the blood, other body fluids, or tissues and which can be used to indicate the presence of some types of cancer). However, it is clear that many will end up being secreted proteins. As in the first phase of the project, the power of World Community Grid will be critical in getting results quickly to researchers in the biological and biomedical communities.

For more information about proteome folding, click here.

Large graphical explanation how Human Proeome folding works.

Mission
The mission of Discovering Dengue Drugs - Together - Phase 2 is to identify promising drug candidates to combat the Dengue, Hepatitis C, West Nile, Yellow Fever, and other related viruses. The extensive computing power of World Community Grid will be used to complete the structure-based drug discovery calculations required to identify these drug candidates.

Significance
This project will discover promising drug candidates that stop the replication of viruses within the Flaviviridae family. Members of this family, including dengue, hepatitis C, West Nile, and yellow fever viruses, pose significant health threats throughout the developed and developing world. More than 40% of the world's population is at risk for infection by dengue virus. Annually, ~1.5 million people are treated for dengue fever and dengue hemorrhagic fever. Hepatitis C virus has infected ~2% of the world's population. Yellow fever and West Nile viruses also have had significant global impact. Unfortunately, there are no drugs that effectively treat these diseases. Consequently, the supportive care necessary to treat these infections and minimize mortality severely strains already burdened health facilities throughout the world. The discovery of both broad-spectrum and specific antiviral drugs is expected to significantly improve global health.

Project Status and Findings:  
Information about the Help Cure Muscular Dystrophy project may be found on these pages, or on the Help Cure Muscular Dystrophy website. To discuss or ask questions about this project, please visit the Help Cure Muscular Dystrophy Forum.

World Community Grid and researchers supported by Decrypthon, a partnership between AFM (French Muscular Dystrophy Association), CNRS (French National Center for Scientific Research), Universite Pierre et Marie Curie, and IBM are investigating protein-protein interactions for more than 2,200 proteins whose structures are known, with particular focus on those proteins that play a role in neuromuscular diseases. The database of information produced will help researchers design molecules to inhibit or enhance binding of particular macromolecules, hopefully leading to better treatments for muscular dystrophy and other neuromuscular diseases.

What is neuromuscular disease and muscular dystrophy?
Neuromuscular disease is a generic term for a group of disorders (more than 200 in all) that impair muscle functioning either directly through muscle pathology (muscular dystrophy) or indirectly through nerve pathology. Most of them are rare (affecting less than one person in 2,000), have a genetic origin (80%) and affect both children and adults. These chronic diseases lead to a decrease in muscle strength, causing serious disabilities in motor functions (moving, breathing etc.). Disease expression is variable; some disorders are progressive, while others remain stable for several years, and the same disease can cause different symptoms from one person to the next.

Despite advances in therapeutic techniques, there is currently no curative treatment available for persons affected by neuromuscular diseases.

We are living in the Age of Energy. The fossil fuel based economy of the present must give way to the renewable energy based economy of the future. Getting there is the grandest challenge humanity faces. Chemistry can help meet this challenge by discovering new materials that efficiently harvest solar radiation, store energy for later use, and reconvert the stored energy when needed.

The Clean Energy project uses computational chemistry and the willingness of people to help look for the best molecules possible for: organic photovoltaics to provide inexpensive solar cells, polymers for the membranes used in fuel cells for electricity generation, and how best to assemble the molecules to make those devices. By helping us search combinatorially among thousands of potential systems, you can contribute to this effort.

Finding better ways to harness sunlight to convert to energy is one of the great challenges of the next century. We are interested in finding not only more efficient solar cells, but also cheaper ones in both energy and cost... Learn more about solar energy science.

We run simulations on thousands of molecules. These include different sizes and also different timescales. That is, we sometimes run single-molecule calculations and also simulations with hundreds of molecues. We obtain can obtain both microscopic and macroscopic properties... Learn more about computational chemistry science.

Project Status and Findings:  
Information about this project is provided on the web pages below. To comment or ask questions about this project, please submit a post in the GO Fight Against Malaria Forum.

Mission
The mission of the GO Fight Against Malaria project is to discover promising drug candidates that could be developed into new drugs that cure drug resistant forms of malaria. The computing power of World Community Grid will be used to perform computer simulations of the interactions between millions of chemical compounds and certain target proteins, to predict their ability to eliminate malaria. The best compounds will be tested and further developed into possible treatments for the disease.

Significance
Malaria is one of the three deadliest infectious diseases on earth and is caused by parasites that infect both humans and animals. Female mosquitoes spread the disease by biting infected hosts and passing the parasites to other hosts that they bite later. When these parasites replicate themselves in red blood cells (which the parasites use for food), the symptoms of malaria appear. Malaria initially causes fevers and headaches, and in severe cases it leads to comas or death. Plasmodium falciparum, the parasite that causes the deadliest form of malaria, kills more people than any other parasite on the planet. Over 3 billion people are at risk of being infected with malaria.

Although there are many approved drugs that are able to cure malarial infections, multi-drug-resistant mutant "superbugs" exist that are not eliminated by the current drugs. Because new mutant superbugs keep evolving and spreading throughout the world, discovering and developing new types of drugs that can cure infections by these multi-drug-resistant mutant strains of malaria is a significant global health priority.

Approach
Scientists at The Scripps Research Institute of La Jolla, California, U.S.A., will use IBM's World Community Grid to computationally evaluate millions of candidate compounds against different molecular drug targets from the malaria parasite. If these target molecules can be disabled, then patients infected with malaria can potentially be cured. The computations will estimate the ability of the candidate compounds to disable the particular target molecules needed by the malaria parasite to survive and multiply. Particular priority will be given to targets and candidate compounds which could attack the multi-drug-resistant mutant "superbug" strains of the malaria parasite. The power of World Community Grid can reduce to one (1) year what would take at least one hundred (100) years to complete using the resources normally available to the researchers at The Scripps Research Institute. The results computed on World Community Grid will be available in the public domain for all scientists to use and build upon in their research to develop drugs to fight malaria.

GO Fight Against Malaria Forum.

Project Status and Findings:  
Information about this project is provided on the web pages below and by the project scientists on the Drug Search for Leishmaniasis website. If you have comments or questions about this project, please visit the Drug Search for Leishmaniasis forum.

Mission
The mission of Drug Search for Leishmaniasis is to identify potential molecule candidates that could possibly be developed into treatments for Leishmaniasis. The extensive computing power of World Community Grid will be used to perform computer simulations of the interactions between millions of chemical compounds and certain target proteins. This will help find the most promising compounds that may lead to effective treatments for the disease.

Significance
Leishmaniasis is one of the most neglected tropical diseases in the world. Each year this disease infects more than two million people in 97 countries. To date, there are no available vaccines to prevent the disease, in spite of multiple research efforts. Leishmaniasis is caused by a protozoan parasite (genus Leishmania) transmitted between human and animal hosts by female sand flies. One form of the disease, the "visceral" form caused by Leishmania infantum in America, mainly affects children, who can die if adequate treatment is not provided promptly. Existing control measures rely upon drug therapy, insect control and education in the affected communities. However, the number of human cases continues to increase in tropical countries such as Bangladesh, India, Sudan, Ethiopia, Brazil, Colombia, Peru and many others.

The classical treatments for all forms of Leishmaniasis can cause severe side effects, including death. Furthermore, drug resistant parasites are causing major problems in many endemic countries. For these reasons, there is an urgent need for new, safe and inexpensive anti-Leishmania drug compounds.

Approach
A software program called VINA from The Scripps Research Institute in La Jolla, California, will be used to perform the virtual chemistry experiments. These virtual experiments will search to find which of millions of drug compounds might be able to disable particular proteins, essential for the parasite's survival. Screening for the best potential drug compounds is an early step in the process of developing effective treatments for the disease. With enough computing power, this screening can be done much more quickly than using conventional laboratory experiments. However, existing computer facilities available to the researchers would require approximately 120 years to perform the screening. The power of World Community Grid can reduce the time required to less than one year. Information about the best candidate compounds will be published by the scientists, and this information will be available in the public domain for other scientists to build upon with their research. Further laboratory work using the best candidates identified by this project could lead to the development of better drugs to fight Leishmaniasis.

Our goal: to understand protein folding, misfolding, and related diseases

What is protein folding?
Proteins are biology's workhorses -- its "nanomachines." Before proteins can carry out these important functions, they assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, in many ways remains a mystery.

Protein folding is linked to disease, such as Alzheimer's, ALS, Huntington's, Parkinson's disease, and many Cancers
Moreover, when proteins do not fold correctly (i.e. "misfold"), there can be serious consequences, including many well known diseases, such as Alzheimer's, Mad Cow (BSE), CJD, ALS, Huntington's, Parkinson's disease, and many Cancers and cancer-related syndromes.

You can help scientists studying these diseases by simply running a piece of software.
Folding@home is a distributed computing project -- people from throughout the world download and run software to band together to make one of the largest supercomputers in the world. Every computer takes the project closer to our goals. Folding@home uses novel computational methods coupled to distributed computing, to simulate problems millions of times more challenging than previously achieved.

What have we done so far?
We have had several successes. You can read about them on our Science page, on our Awards page, or go directly to our Results page.

 Folding@Home on You Tube.

Volunteer computing for biomedicine

GPUGRID.net is a novel distributed supercomputing infrastructure made of many NVIDIA graphics cards joined together to deliver high-performance all-atom biomolecular simulations. The molecular simulations performed by our volunteers are some of the most common types performed by scientists in the field, but they are also some of the most computationally demanding and usually require a supercomputer.
Running GPUGRID on GPUs innovates volunteer computing by delivering supercomputing class applications on a cost effective infrastructure which will greatly impact the way biomedical research is performed.