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  • richardmitnick 11:20 am on July 18, 2014 Permalink | Reply
    Tags: , , , , Rosetta@home   

    From Rosetta@home 



    Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s (See our Disease Related Research for more information). Please join us in our efforts! Rosetta@home is not for profit.

    About Rosetta

    One of the major goals of Rosetta is to predict the shapes that proteins fold up into in nature. Proteins are linear polymer molecules made up of amino acid monomers and are often refered to as “chains.” Amino acids can be considered as the “links” in a protein “chain”. Here is a simple analogy. When considering a metal chain, it can have many different shapes depending on the forces exerted upon it. For example, if you pull its ends, the chain will extend to a straight line and if you drop it on the floor, it will take on a unique shape. Unlike metal chains that are made of identical links, proteins are made of 20 different amino acids that each have their own unique properties (different shapes, and attractive and repulsive forces, for example), and in combination, the amino acids exert forces on the chain to make it take on a specific shape, which we call a “fold.” The order in which the amino acids are linked determines the protein’s fold. There are many kinds of proteins that vary in the number and order of their amino acids.

    To predict the shape that a particular protein adopts in nature, what we are really trying to do is find the fold with the lowest energy. The energy is determined by a number of factors. For example, some amino acids are attracted to each other so when they are close in space, their interaction provides a favorable contribution to the energy. Rosetta’s strategy for finding low energy shapes looks like this:

    Start with a fully unfolded chain (like a metal chain with its ends pulled).
    Move a part of the chain to create a new shape.
    Calculate the energy of the new shape.
    Accept or reject the move depending on the change in energy.
    Repeat 2 through 4 until every part of the chain has been moved a lot of times.

    We call this a trajectory. The end result of a trajectory is a predicted structure. Rosetta keeps track of the lowest energy shape found in each trajectory. Each trajectory is unique, because the attempted moves are determined by a random number. They do not always find the same low energy shape because there are so many possibilities.

    A trajectory may consist of two stages. The first stage uses a simplified representation of amino acids which allows us to try many different possible shapes rapidly. This stage is regarded as a low resolution search and on the screen saver you will see the protein chain jumping around a lot. In the second stage, Rosetta uses a full representation of amino acids. This stage is refered to as “relaxation.” Instead of moving around a lot, the protein tries smaller changes in an attempt to move the amino acids to their correct arrangment. This stage is regarded as a high resolution search and on the screen saver, you will see the protein chain jiggle around a little. Rosetta can do the first stage in a few minutes on a modern computer. The second stage takes longer because of the increased complexity when considering the full representation (all atoms) of amino acids.

    Your computer typically generates 5-20 of these trajectories (per work unit) and then sends us back the lowest energy shape seen in each one. We then look at all of the low energy shapes, generated by all of your computers, to find the very lowest ones. This becomes our prediction for the fold of that protein.

    To join this project, download and install the BOINC software on which it runs. Then attach to the project. While you are at BOINC, look at some of the other projects to see what else might be of interest to you.

    Rosetta screensaver


    ScienceSprings is powered by MAINGEAR computers

  • richardmitnick 11:33 am on June 27, 2012 Permalink | Reply
    Tags: , , , , , Rosetta@home   

    From Argonne Lab APS: “Computer-Designed Proteins to Disarm a Variety of Flu Viruses” 

    News from Argonne National Laboratory

    JUNE 18, 2012
    No Writer Credit

    Computer-designed proteins are under construction to fight the flu. Researchers who carried out studies at the U.S. Department of Energy Office of Science’s Advanced Photon Source at Argonne National Laboratory are demonstrating that proteins that are found in nature, but do not normally bind the influenza virus, can be engineered to act as broad-spectrum antiviral agents against a variety of flu virus strains, including the H1N1 pandemic influenza.

    Close-up view of the F-HB80.4-SC1918/hemagglutinin interface as determined at . From T.A. Whitehead et al., Nat. Biotech. 30(6), 543 (6 June 2012).

    ‘One of these engineered proteins has a flu-fighting potency that rivals that of several human monoclonal antibodies,’ said David Baker, professor of Biochemistry at the University of Washington, in a report in Nature Biotechnology.

    The research team in this study, from the University of Washington, The Scripps Research Institute, and the Naval Health Research Center is making major inroads in optimizing the function of computer-designed influenza inhibitors. These proteins are constructed via computer modeling to fit exquisitely into a specific nano-sized target on flu viruses. By binding the target region like a key into a lock, they keep the virus from changing shape, a tactic that the virus uses to infect living cells. The research efforts, akin to docking a space station but on a molecular level, are made possible by computers that can describe the landscapes of forces involved on the submicroscopic scale.”

    Dr David Baker heads up the Baker Laboratory at The University of Washington. The Baker Lab is the home of the Rosetta@home project, a Public Distributed Computing project which runs on BOINC software. Rosetta research studies “… the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases…” using the combined resources of thousands of personal computers at home and at work, which give over their unused CPU cycles for the processing of data.

    See the full article here.

    Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy’s Office of Science

  • richardmitnick 8:43 pm on June 13, 2012 Permalink | Reply
    Tags: , , , , Rosetta@home, , ,   

    From Berkeley Lab: “Berkeley Lab Scientists Help Define the Healthy Human Microbiome” 

    Berkeley Lab

    Computing, bioinformatics, and microbial ecology resources play key role in mapping our microbial make-up

    June 13, 2012
    Dan Krotz

    You’re outnumbered. There are ten times as many microbial cells in you as there are your own cells.

    The human microbiome—as scientists call the communities of microorganisms that inhabit your skin, mouth, gut, and other parts of your body by the trillions—plays a fundamental role in keeping you healthy. These communities are also thought to cause disease when they’re perturbed. But our microbiome’s exact function, good and bad, is poorly understood. That could change.

    The bacterium, Enterococcus faecalis, which lives in the human gut, is just one type of microbe studied in NIH’s Human Microbiome Project. (Courtesy: United States Department of Agriculture)

    A National Institutes of Health (NIH)-organized consortium that includes scientists from the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) has for the first time mapped the normal microbial make-up of healthy humans. [Human Microbiome Project (HMP) is a United States National Institutes of Health initiative with the goal of identifying and characterizing the microorganisms which are found in association with both healthy and diseased humans (i.e. their microbial flora). Launched in 2008, it is a five-year project, best characterized as a feasibility study, and has a total budget of $115 million. The ultimate goal of this and similar NIH-sponsored microbiome projects is to test if changes in the human microbiome are associated with human health or disease. This topic is currently not well-understood.]

    The research will help scientists understand how our microbiome carries out vital tasks such as supporting our immune system and helping us digest food. It’ll also shed light on our microbiome’s role in diseases such as ulcerative colitis, Crohn’s disease, and psoriasis, to name a few.”

    See the full article here.

    For those interested – and you should be interested – the Human Protein Folding Project (HPF2) at the Bonneau Lab, New York University, is a participant in the HMP project. HPF2 is a project in Public Distributed Computing under the aegis of the World Community Grid (WCG), running on software from the Berkeley Open Infrastructure for Network Computing (BOINC) and using the project products of the rosetta@home project from the Baker Lab, University of Washington.

    That is a pretty long sentence. What it means is, if you visit WCG, or BOINC, and download the BOINC agent software for Windows, Linux, or Mac, you can attach to the HPF2 project and process data for HMP. While you are at it, look around at WCG website, there are about a dozen very worthwhile projects all aimed at curing illnesses and solving fundamental problems for mankind. Also, at the BOINC website the are a vast variety of projects in Biology, Chemistry, Physics, Mathematics, and Astronomy.

    Here are some pretty pictures.

    So, you know, when you see graphics, these are serious guys. Give them (us) a look.

    My BOINC stats.

  • richardmitnick 1:03 pm on April 30, 2012 Permalink | Reply
    Tags: , , , , , Dr. David Baker, , Rosetta@home   

    From David Baker at Rosetta@home: Rosetta Chosen for the BOINC Pentathlon 

    This is a post from Dr. David Baker, The Baker Lab at the University of Washington, the site of rosetta@home.

    Dr. David Baker

    “I have just been told the very good news that Rosetta@home will be the first project of the BOINC pentathlon, and would like to thank all of the participating teams. I also just learned from the discussion thread that Rosetta@home will be the project of the month for BOINC synergy-this is more excellent news!!

    Your increased contributions to rosetta@home could not come at a better time! We’ve been testing our improved structure prediction methodology in a recently started challenge called CAMEO. For most of the targets, the Rosetta@home models are extremely good, but for a minority of targets the predictions are not good at all. We’ve now tracked down the source of these failures and it is what we are calling “workunit starvation”; in the limited amount of time the Rosetta server has to produce models (2-3 days) in these cases very few models were made-this happens because many targets are being run on the server so that only a fraction of your cpu power is focused on any one target. while we are working to fix this internally, by far the best solution is to have more total CPU throughput so each target gets more models.

    You can follow how we are doing at http://www.cameo3d.org/. You will see that Rosetta is one of the few servers whose name is not kept secret-this is because Rosetta is a public project. Our server receives targets from CAMEO and soon CASP, sends the required calculations out to your computers through Rosetta@home, and then processes the returned results and submits the lowest energy models.

    We are excited that the workunit starvation problem may go away through your increased efforts for Rosetta@home. Thanks!!!”

    David’s post is here.


    BOINC is a leader in the field(s) of Distributed Computing, Grid Computing and Citizen Cyberscience.BOINC is more properly the Berkeley Open Infrastructure for Network Computing, developed at UC Berkeley.

    Visit the BOINC web page, click on Choose projects and check out some of the very worthwhile studies you will find. Then click on Download and run BOINC software/ All Versons. Download and install the current software for your 32bit or 64bit system, for Windows, Mac or Linux. When you install BOINC, it will install its screen savers on your system as a default. You can choose to run the various project screen savers or you can turn them off. Once BOINC is installed, in BOINC Manager/Tools, click on “Add project or account manager” to attach to projects. Many BOINC projects are listed there, but not all, and, maybe not the one(s) in which you are interested. You can get the proper URL for attaching to the project at the projects’ web page(s) BOINC will never interfere with any other work on your computer.


    SETI@home The search for extraterrestrial intelligence. “SETI (Search for Extraterrestrial Intelligence) is a scientific area whose goal is to detect intelligent life outside Earth. One approach, known as radio SETI, uses radio telescopes to listen for narrow-bandwidth radio signals from space. Such signals are not known to occur naturally, so a detection would provide evidence of extraterrestrial technology.

    Radio telescope signals consist primarily of noise (from celestial sources and the receiver’s electronics) and man-made signals such as TV stations, radar, and satellites. Modern radio SETI projects analyze the data digitally. More computing power enables searches to cover greater frequency ranges with more sensitivity. Radio SETI, therefore, has an insatiable appetite for computing power.

    Previous radio SETI projects have used special-purpose supercomputers, located at the telescope, to do the bulk of the data analysis. In 1995, David Gedye proposed doing radio SETI using a virtual supercomputer composed of large numbers of Internet-connected computers, and he organized the SETI@home project to explore this idea. SETI@home was originally launched in May 1999.”

    SETI@home is the birthplace of BOINC software. Originally, it only ran in a screensaver when the computer on which it was installed was doing no other work. With the powerand memory available today, BOINC can run 24/7 without in any way interfering with other ongoing work.

    The famous SET@home screen saver, a beauteous thing to behold.

    einstein@home The search for pulsars. “Einstein@Home uses your computer’s idle time to search for weak astrophysical signals from spinning neutron stars (also called pulsars) using data from the LIGO gravitational-wave detectors, the Arecibo radio telescope, and the Fermi gamma-ray satellite. Einstein@Home volunteers have already discovered more than a dozen new neutron stars, and we hope to find many more in the future. Our long-term goal is to make the first direct detections of gravitational-wave emission from spinning neutron stars. Gravitational waves were predicted by Albert Einstein almost a century ago, but have never been directly detected. Such observations would open up a new window on the universe, and usher in a new era in astronomy.”

    MilkyWay@Home Milkyway@Home uses the BOINC platform to harness volunteered computing resources, creating a highly accurate three dimensional model of the Milky Way galaxy using data gathered by the Sloan Digital Sky Survey. This project enables research in both astroinformatics and computer science.”

    Leiden Classical “Join in and help to build a Desktop Computer Grid dedicated to general Classical Dynamics for any scientist or science student!”

    World Community Grid (WCG) World Community Grid is a special case at BOINC. WCG is part of the social initiative of IBM Corporation and the Smarter Planet. WCG has under its umbrella currently eleven disparate projects at globally wide ranging institutions and universities. Most projects relate to biological and medical subject matter. There are also projects for Clean Water and Clean Renewable Energy. WCG projects are treated respectively and respectably on their own at this blog. Watch for news.

    Rosetta@home “Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s….”

    GPUGrid.net “GPUGRID.net is a distributed computing infrastructure devoted to biomedical research. Thanks to the contribution of volunteers, GPUGRID scientists can perform molecular simulations to understand the function of proteins in health and disease.” GPUGrid is a special case in that all processor work done by the volunteers is GPU processing. There is no CPU processing, which is the more common processing. Other projects (Einstein, SETI, Milky Way) also feature GPU processing, but they offer CPU processing for those not able to do work on GPU’s.

    These projects are just the oldest and most prominent projects. There are many others from which you can choose.

    There are currently some 300,000 users with about 480,000 computers working on BOINC projects That is in a world of over one billion computers. We sure could use your help.

    My BOINC


  • richardmitnick 2:46 pm on March 30, 2012 Permalink | Reply
    Tags: , , , , David Baker, , Rosetta@home   

    From David Baker at the Rosetta Project – We Need Your Help 

    Dr David baker
    Dr David Baker, Forum moderator, Project administrator, Project developer, Project scientist

    David Baker tells us,

    “In the last two months we believe we have made quite a breakthrough in structure prediction, and are excited to test the new method in CASP10. We need your help though–we are now testing many aspects of the new approach and are seriously limited by available CPU cycles. There are now so many flu inhibitor design and structure prediction jobs queued up on Rosetta@Home that there is an eight day wait before they are getting sent out to you. This would be a great time to temporarily increase Rosetta@Home’s share on your computers and/or recruit new users–we need all the help we can get! thanks! David”

    From The Rosetta web site:

    Rosetta@home needs your help to determine the 3-dimensional shapes of proteins in research that may ultimately lead to finding cures for some major human diseases. By running the Rosetta program on your computer while you don’t need it you will help us speed up and extend our research in ways we couldn’t possibly attempt without your help. You will also be helping our efforts at designing new proteins to fight diseases such as HIV, Malaria, Cancer, and Alzheimer’s (See our Disease Related Research [below] for more information). Please join us in our efforts! Rosetta@home is not for profit.

    Disease Related Research

    Comments from David Baker

    “My research group is involved both in fundamental methods development research and in trying to fight disease more directly. Most of the information on this site focuses on basic research, but I thought you might be interested in hearing about some of the disease related work we are doing that you will be contributing to at Rosetta@home.

    Malaria: We are part of a collaborative project headed by Austin Burt at Imperial College in London that is one of the Gates Foundation “Grand Challenge Projects in Global Health”. Malaria is caused by a parasite that spends part of its life cycle inside the mosquito, and is passed along to humans by mosquito bites. The idea behind the project is to make mosquitoes resistant to the parasite by eliminating genes required in the mosquito for the parasite to live. Our part of the project is to use our computer based design methods (ROSETTA) to engineer new enzymes that will specifically target and inactivate these genes.

    Anthrax: We are using ROSETTA to help John Collier’s research group at Harvard build models of anthrax toxin that should contribute to the development of treatments. You can read the abstract of a paper describing some of this work at http://www.pnas.org/cgi/content/abstract/102/45/16409

    HIV: One of the reasons that HIV is such a deadly virus is that it has evolved to trick the immune system. We are collaborating with researchers in Seattle and at the NIH to try to develop a vaccine for HIV. Our role in this project is central–we are using ROSETTA to design small proteins that display the small number of critical regions of the HIV coat protein in a way that the immune system can easily recognize and generate antibodies to. Our goal is to create small stable protein vaccines that can be made very cheaply and shipped all over the world.

    Other viruses: We have been collaborating with Pam Bjorkman’s laboratory at Cal Tech to use the ROSETTA protein-protein docking methodology to build models of herpes simplex virus proteins in complex with human proteins.

    Alzheimer’s disease: Alzheimer’s and many other diseases are likely to be caused by abberant protein folding in which proteins form large aggregated structures called amyloids rather than folding up into their normal biologically active states. A big advance was made recently by David Eisenberg’s research group at UCLA in solving the first structure of an amyloid. We are collaborating with their research group to use the structure to predict which parts of proteins are likely to form amyloids, which will be a first step to blocking amyloid formation and hopefully disease.

    Cancer: Cancer can be caused by mutations in key genes that disrupt normal cellular control processes. We are developing methods for cutting DNA at specific sites in the genome, and we will be targeting sites that are implicated in cancer. After these sites are cut, they should be repaired by the cell using a second, unmutated copy of the gene and the cell should no longer be cancerous. This is a very specific form of gene therapy that, if successful, will circumvent one the main objections to current gene therapy methods; namely, current methods insert the unmutated copy of a gene randomly into the genome, and if the insertion point happens to be near an oncogene, the gene therapy will cure one disease but cause another. Because our methods will target specific sites instead of random sites, they should avoid this pitfall.

    Prostate Cancer: The androgen receptor (AR) binds testosterone and is responsible for normal male development. When the AR becomes hypersensitive to testosterone, prostate cancer is the result. The current treatment for prostate cancer, called “hormone therapy”, involves lowering the amount of testosterone available (sometimes by castration). Many malignant tumors are resistant to this therapy, however, so we are applying our protein design methodology to find different ways to inhibit the AR and to treat prostate cancer. Specifically, we are trying to design proteins that will disable the AR even in the presence of testosterone. We are doing this by designing proteins that will prevent the AR from entering the nucleus of the cell (which is where it does its dirty work), and also preventing it from binding DNA and activating tumor-specific genes even if it does get into the nucleus.

    The above projects are not currently running on BOINC because we don’t yet have an efficient queuing system which lets people submit jobs easily, but look for them soon! Also, rest assured that the structure prediction calculations currently running on your computers will have direct bearing on treating disease. There is a three-fold explanation for this direct relationship between structure prediction and disease treatment:

    Structure prediction and protein design are closely related.

    Improvements in structure prediction lead to improvements in protein design, which in turn can be directly translated into making new enzymes, vaccines, etc. For more information on protein design you might be interested in looking at the review we recently wrote in science which is available at our home page (http://depts.washington.edu/bakerpg).

    Schueler-Furman, O., Wang, C., Bradley, P., Misura, K., Baker, D. (2005). Progress in modeling of protein structures and interactions Science 310, 638-642.

    Structure prediction identifies targets for new drugs.

    When we predict structures for proteins in the human genome on a large scale, we learn about the functions of many proteins, which will help in understanding how cells work and how disease occurs. More directly, we will be able to identify many new potential drug targets for which small molecule inhibitors (drugs) can be designed. To put this in context, one major road-block to developing new treatments for human disease is identifying new “drugable” protein targets. Most new drugs these days interact with the same targets as the old drugs, so these drugs lead to only small improvements in disease treatment. Structure prediction helps us identify new drug targets, and so will help us find innovative, perhaps even breakthrough, treatments for disease.

    Structure prediction allows us to use “rational design” to create new drugs.

    If we know the structure of a protein, we can determine its functional sites, and specifically target those sites to be inactivated by a new drug. Calculation of whether a small molecule (drug) will bind to and inactivate a protein target is similar in many ways to the structure prediction calculations we are doing here–it is basically a problem of finding the lowest energy structure of the protein plus drug system–and we have recently developed a new module in ROSETTA to do this docking problem. Results are very promising, and in the near future your machines will likely be running drug docking calculations along with the vaccine and therapeutic protein design projects described above, in addition to the protein folding calculations you are doing now.

    Please visit the Baker Lab web site to read about

    Computational redesign of a mononuclear zinc metalloenzyme for organophosphate hydrolysis

    Increased Diels-Alderase activity through backbone remodeling guided by Foldit players

    Algorithm discovery by protein folding game players

    Crystal structure of a monomeric retroviral protease solved by protein folding game players

    Computational design of protein inhibitors of Spanish and avian flu hemagglutinin



    Rosetta@home runs on BOINC software from U.C. Berkeley

  • richardmitnick 9:32 am on December 6, 2011 Permalink | Reply
    Tags: , , , Rosetta@home, , ,   

    From the New York Times: “Computer Scientists May Have What It Takes to Help Cure Cancer” – Another Blown Opportunity to boost BOINC 

    December 5, 2011

    This is copyright protected, so just a couple of hints.
    “The war against cancer is increasingly moving into cyberspace. Computer scientists may have the best skills to fight cancer in the next decade — and they should be signing up in droves….An inspirational example is the Foldit game — developed by the computer scientist Zoran Popovic at the University of Washington.

    Very nice, great article, but, huge gap. No mention of the roots of Dr Popovic’s successful adventure.

    Dr Popovic worked with The Baker Laboratory, the locus of rosetta@home, a project which runs on BOINC software from UC Berkeley. Rosetta@home has currently 37,456 “users” on 60162 “hosts”. The project does currently 58 TeraFLOPS of data per 24 hour period.

    On the one hand, you can certainly visit the Foldit web site to participate. If, on the other hand, you are not fond of games, you can visit the BOINC web site, download and install the small piece of software, and attach to the Rosetta project. You will receive small packs of data called “work units” or “WU’s” to “crunch”. As each WU is finished, your computer will return the results and you will receive more work.

    Rosetta software is also used by World Community Grid (WCG) project Human Proteome Folding. This project is based at New York University in the Bonneau Laboratory


    At both the WCG and BOINC web sites you will find many other really exciting projects in which you may participate. All WCG projects run on the BOINC software, along with the many independent projects at the BOINC web site.

    Once you have installed the BOINC software and attached to your chosen projects, you can be as active or passive in this process as you wish. You can pretty much simply let the stuff happen in the background and pay it scant attention. However, each project has its own forum covering many topics, including the science involved and the operation of the software. You can also check to see how your are doing by signing on at BOINCstats.com

    There are currently 286,105 “users” (people) on 515,015 “hosts” (computers) in all of BOINC. Currently we are doing 5,337 TeraFLOPS of work in a 24 hour period. That’s over half a PetafLOP, which would put us somewhere around 14th or 15th on the TOP500 list of supercomputers in the world. Except, in that world, we don’t count. WCG currently has 94,007 users on 211,163 hosts. We are currently at 278 TeraFLOPS.

    BOINC software will run on Windows, Mac and Linux based computers. So, whatever your flavor, why don’t you visit BOINC and WCG, give us a look, and try us out? The BOINC process never interferes with anything else that you are doing on the computer. If on occasion you require huge amounts of resources, such as “storming the castle”, BOINC will instantaneously give up its resources and pause until your battle is finished. I hope to run into you in a forum.

    Mr. Patterson work is an example of why I started this blog.

  • richardmitnick 5:29 pm on November 25, 2011 Permalink | Reply
    Tags: , , , , Rosetta@home, , ,   

    From WCG Project Human Proteome Folding (HPF2) Exciting Updates 

    Human Proteome Folding (HPF2)., a WCG project in The Bonneau Lab at New York University has posted some very exciting news. The report is copyright protected, so I will not trespass on that.

    Depictions of proteins

    HPF2 utilizes software developed by BOINC project Rosetta@home, in the The Baker Lab at University of Washington.

    You can see the report here.

    But WCG crunchers can be proud of the fact that we have contributed – this from the WCG web site – 96,695 years, 223 days, 09 hours,26 minutes, 30 seconds to this effort. This is the power of Public Distributed Computing via the BOINC software on which our projects are run.

    I cannot begin to contemplate how this work would have gotten to this point without us, except at the expensive cost of processing time on some supercomputer.


    You, too, dear reader, can be a part of this incredible process. Visit either WCG or BOINC, download and install the software, and attach to this and other worthy projects at the WCG web site and also at the BOINC website. You financial cost is about the same as a 100-150 watt light bulb. Your personal satisfaction at being a part of this is immeasurable.

  • richardmitnick 11:04 am on September 19, 2011 Permalink | Reply
    Tags: , , , Rosetta@home   

    The Rosetta project points us to The Scientist article about Rosetta’s Foldit 


    David Baker of the Baker Lab tells us “Today’s issue of Nature Structural Biology reports the determination of the structure of a protein by FoldIt players. This is exciting because it is perhaps the first example of a long standing scientific problem solved by non-scientists. You might read about this in your newspaper; here is a report that does a good job in explaining how FoldIt came out of Rosetta@home…”

    “Public Solves Protein Structure
    Players of an online game that allows users to adjust how proteins are folded have solved a decade-long protein structure mystery.”

    See the article here.

    Rosetta@home runs on BOINC software from UC Berkeley

  • richardmitnick 4:06 pm on April 10, 2011 Permalink | Reply
    Tags: , , , , , , , , Rosetta@home,   

    WCG: An Overview 

    World Community Grid

    WCG tells us: “World Community Grid brings people together from across the globe to create the largest non-profit computing grid benefiting humanity. It does this by pooling surplus computer processing power. We believe that innovation combined with visionary scientific research and large-scale volunteerism can help make the planet smarter. Our success depends on like-minded individuals – like you.”

    “We are now partnering with People for a Smarter Planet, a collective of communities that let you make a personal difference in solving some of the world’s toughest challenges. Please show your support by clicking the Like button on their Facebook page.


    World Community Grid operates under the watchful eye and with the financial support of IBM Corporation.


    Here is what IBM says: “Our World Community Grid initiative utilizes grid computing technology to harness the tremendous power of idle computers to perform specific computations related to critical research around complex biological, environmental and health-related issues. The current projects include Help Fight Childhood Cancer, Clean Energy, and Nutritious Rice for the World, FightAIDS@Home, Help Conquer Cancer, AfricanClimate@Home, and a genomics initiative and research on Dengue Fever.

    Lets look at some of these projects. All of the text for each project comes from the project’s page at WCG.

    Computing for Clean Water


    The mission of Computing for Clean Water is to provide deeper insight on the molecular scale into the origins of the efficient flow of water through a novel class of filter materials. This insight will in turn guide future development of low-cost and more efficient water filters.

    Lack of access to clean water is one of the major humanitarian challenges for many regions in the developing world. It is estimated that 1.2 billion people lack access to safe drinking water, and 2.6 billion have little or no sanitation. Millions of people die annually – estimates are 3,900 children a day – from the results of diseases transmitted through unsafe water, in particular diarrhea.

    Technologies for filtering dirty water exist, but are generally quite expensive. Desalination of sea water, a potentially abundant source of drinking water, is similarly limited by filtering costs. Therefore, new approaches to efficient water filtering are a subject of intense research. Carbon nanotubes, stacked in arrays so that water must pass through the length of the tubes, represent a new approach to filtering water.”

    This projects partners with CNMM, the Center for Nano and Micro Mechanics at Tsinghua University in Beijing, China


    The Clean Energy Project


    The mission of The Clean Energy Project is to find new materials for the next generation of solar cells and later, energy storage devices. By harnessing the immense power of World Community Grid, researchers can calculate the electronic properties of hundreds of thousands of organic materials – thousands of times more than could ever be tested in a lab – and determine which candidates are most promising for developing affordable solar energy technology.

    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, but getting there is one of the greatest 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 search combinatorially among thousands of potential systems, World Community Grid volunteers are contributing to this effort.”

    Discovering Dengue Drugs – Together


    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.

    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.”

    Help Cure Muscular Dystrophy


    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.

    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.”

    Help Conquer Cancer


    The mission of Help Conquer Cancer is to improve the results of protein X-ray crystallography, which helps researchers not only annotate unknown parts of the human proteome, but importantly improves their understanding of cancer initiation, progression and treatment.

    In order to significantly impact the understanding of cancer and its treatment, novel therapeutic approaches capable of targeting metastatic disease (or cancers spreading to other parts of the body) must not only be discovered, but also diagnostic markers (or indicators of the disease), which can detect early stage disease, must be identified.

    Researchers have been able to make important discoveries when studying multiple human cancers, even when they have limited or no information at all about the involved proteins. However, to better understand and treat cancer, it is important for scientists to discover novel proteins involved in cancer, and their structure and function.

    Scientists are especially interested in proteins that may have a functional relationship with cancer. These are proteins that are either over-expressed or repressed in cancers, or proteins that have been modified or mutated in ways that result in structural changes to them.

    Improving X-ray crystallography will enable researchers to determine the structure of many cancer-related proteins faster. This will lead to improving our understanding of the function of these proteins and enable potential pharmaceutical interventions to treat this deadly disease.”

    Human Proteome Folding


    “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.”



    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.”


    There are currently about 98,000 members of this crunching community. We are called crunchers because that is what our computers do. Once having installed the software and chosen our projects, we are sent small work units to process. The finished data is sent back to WCG and we get new work units. How are we rewarded for our efforts? Really, just with the satisfactiuon of knowing that we might be helping to save lives. But, we do get little gifts, badges based upon our completed work. Some crunchers have organized themselves into teams. The teams compete for points or credits. There are al;l sorts of teams, from a few people organizing in a church or synagogue, to mega teams of techies building mroe and more Linux boxes.

    So, 98,000. That is a lot of people; but not in a world with one billion computers. We want and need your help. I am personally crunching 24/7 on five machines – yesterday the sixth, an older PC died.
    The cost in electricity? About the same as a 100-150 watt light bulb as long as you have your monitor on a power save setting.

    All WCG projects run on software developed and continually upgraded by At UC Berkeley, The Berkeley Open Infrastructure for Network Computing.You can download the little piece of BOINC software that makes this all happen either at WCG or http://boinc.berkeley.edu/.

    If you choose to download the software at the BOINC page, there you will see a link to a whole other list of wonderful projects which are running independently of WCG.

    So, please, won’t you give us a look?

  • richardmitnick 11:30 am on January 11, 2011 Permalink | Reply
    Tags: , , , Rosetta@home,   

    From PNNL Labs 

    Finally some good news from a US D.O.E. Lab in 2011.

    Sequenced Genomes Make Good Neighbors

    Comparing mass spectra among organisms enables protein identification

    “To study the proteomes of organisms, a first step often involves using sequenced genomes in conjunction with mass spectrometric measurements for global protein identifications. But, how do you identify the proteins in an organism yet to be sequenced? One way is to look at its sequenced neighbors, which is what scientists at Pacific Northwest National Laboratory (PNNL) did. They demonstrated a trans-organism search strategy for determining the extent to which near-neighbor genome sequences can be effective for global protein identifications in unsequenced organisms isolated from environmental samples.

    In this strategy, mass spectra from an unsequenced organism were searched against the genome sequences for progressively more genetically distant neighbor organisms to determine how much proteome information could be obtained about one species when using the genomic sequence of another. The work appeared in PLoS ONE in November 2010.

    Protein identifications from Columbia River isolates are mapped to the reference genomes of S. oneidensis MR-1 (A) and S. putrefaciens CN32 (B). While all organisms were grown under the same conditions, observation of no protein expression compared to the reference proteome reveals these organisms have undergone evolutionary divergence. The protein identifications for each of the Shewanella species mapped onto their respective genomes, as well as the protein orthologs across species, also are shown. Two regions of “missing” proteome information from the Hanford Reach isolates are highlighted.

    Read the full article here.

    I might also point here to the World Community Grid (WCG) project in Human Proteome Folding (hpf2). WCG projects employ thousands of individual computer users and their machines to “crunch” data in what is called Public Distributed Computing. These projects run on software from Berkeley Open Infrastructure for Network Computing (BOINC). In fact, hpf2 uses software developed by a BOINC project, Rosetta@home , which is based in the Baker Lab at the University of Washington.

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