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  • richardmitnick 4:49 pm on January 20, 2016 Permalink | Reply
    Tags: , Baker Lab, ,   

    From Science Node: “Solving a protein puzzle” 

    Science Node bloc
    Science Node

    20 Jan, 2016
    Greg Moore

    Temp 1
    Stacking up the proteins. After decades of attempts, scientists finally succeeded in unraveling the TIM-barel protein. Here is a graphic depiction of how their simulations fared against the Astral SCOPe 2.04 database. Courtesy Po-Ssu Huang.

    Computational models open up new possibilities for designing proteins for targeted disease treatment. Using the Open Science Grid (OSG), Baker Lab researchers at the University of Washington have simulated a protein that has stymied scientists for the last 25 years, and have opened the way for a new generation of custom-designed enzymes.

    The cylindrical TIM-barrel (triosephosphate isomerase-barrel) protein occurs widely in enzymes and is an attractive goal for research. But ever since it was first targeted in a European Molecular Biology Organization workshop on protein design in 1987, modeling this structure has been an elusive goal. Even the shortest TIM-barrel structure is highly complex.

    Now, thanks to OSG resources, the Baker Lab has generated large numbers of TIM-barrel structures as starting points for enzyme design calculations. Published in Nature Chemical Biology, their results will aid de novo design of custom-made catalysts or binders without the need to negotiate the structural complexity of naturally occurring proteins.

    To scale up simulations for the TIM-barrel computational model, the research team used the OSG, which is supported by the US National Science Foundation and the US Department of Energy’s Office of Science.

    “The massive computing power of the OSG allowed us to quickly get answers,” says Po-Ssu Huang, one of the lead researchers on the paper and a research scientist at the Baker Lab. In the past year, the researchers used an average of 46,000 core OSG hours per week — a total of around 2.4 million core hours.

    “Baker Lab has its own local HTCondor submit host that is connected to the OSG virtual organization HTCondor infrastructure,” says Mats Rynge, a computer scientist at the Information Sciences Institute of the University of Southern California and a member of the OSG User Support team. “Jobs submitted on the host are automatically scheduled onto available resources across the OSG.”

    Temp 2
    Stability comparisons. Strands are sequentially colored from blue to red, and for the orange layer configurations, side chain packing is shown with space-fill spheres. The stabilities of the six different variants correlate strongly with the configurations in the hydrophobic packing layer. Courtesy Po-Ssu Huang.

    The benefit of this setup (submit locally, compute globally) is that a group can maintain their local host – and still manage users, access, and upgrades – but not have to worry about maintaining the entire OSG computing infrastructure.

    “What we do involves computational algorithms, but at the same time everything we design is actually tested here in the lab. We take virtual simulations to practical applications — turning these molecules into new functional molecules for the real world,” says Huang. “The TIM-barrel computational model is an example of taking what we learn to build new proteins for other applications.”

    Applications include disease sensors and drug detectors using proteins as binders for small molecules.

    “The Holy Grail here is to understand enough to build new things,” Huang says. “This breakthrough has implications for neuroscience, industrial applications, biotech, enzymes for drug delivery, vaccines for HIV, and proteins that can inhibit Ebola. It’s just a huge field. This is where computer simulation comes in, and the faster the better. The OSG definitely fits the need.”

    See the full article here .

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    Science Node is an international weekly online publication that covers distributed computing and the research it enables.

    “We report on all aspects of distributed computing technology, such as grids and clouds. We also regularly feature articles on distributed computing-enabled research in a large variety of disciplines, including physics, biology, sociology, earth sciences, archaeology, medicine, disaster management, crime, and art. (Note that we do not cover stories that are purely about commercial technology.)

    In its current incarnation, Science Node is also an online destination where you can host a profile and blog, and find and disseminate announcements and information about events, deadlines, and jobs. In the near future it will also be a place where you can network with colleagues.

    You can read Science Node via our homepage, RSS, or email. For the complete iSGTW experience, sign up for an account or log in with OpenID and manage your email subscription from your account preferences. If you do not wish to access the website’s features, you can just subscribe to the weekly email.”

  • richardmitnick 11:33 am on June 27, 2012 Permalink | Reply
    Tags: , , Baker Lab, , ,   

    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 1:03 pm on April 30, 2012 Permalink | Reply
    Tags: , Baker Lab, , , , Dr. David Baker, ,   

    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 11:04 am on September 19, 2011 Permalink | Reply
    Tags: , Baker Lab, ,   

    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

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