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  • richardmitnick 9:29 am on July 4, 2018 Permalink | Reply
    Tags: BOINC-Berkeley Open Infrastructure for Network Computing, Carbon nanostructures, ,   

    From World Community Grid (WCG): “The Expanding Frontiers of Carbon Nanotube Technology” 

    New WCG Logo

    WCGLarge

    From World Community Grid (WCG)

    3 Jul 2018

    Summary
    The Clean Water Project made an exciting discovery about the possible applications of carbon nanostructures to water purification, biomedical research, and energy research. Dr. Ming Ma, one of the scientists on the project, recently published a paper that summarizes the current status of work in this field.

    1
    The team at Tsinghua University includes (left to right) Ming Ma, Kunqi Wang, Wei Cao, and Jin Wang. Not pictured: Yao Cheng

    Dr. Ming Ma (of the Computing for Clean Water project) at Tsinghua University recently published a paper in the Journal of Micromechanics and Microengineering entitled “Carbon nanostructure based mechano-nanofluidics.” The paper is a thorough survey of all the recent research work on fluid flow in carbon nanostructures, such as carbon nanotubes and graphene sheets.

    Carbon atoms can form single-atom thick sheets known as graphene. When these are rolled into tube shape, they are called carbon nanotubes. In recent years, there has been a flurry of research work with these nanostructures, called that because they deal with very tiny atomic structures measured in nanometers (billionths of a meter). The Computing for Clean Water project is one example of recent research in this area: By using World Community Grid to simulate water flow through carbon nanotubes at an unprecedented level of detail, the project’s research team discovered that under specific conditions, certain kinds of natural vibrations of atoms inside the nanotubes can lead to a 300% increased rate of diffusion (a kind of flow) of water through the nanotubes.

    Among their many surprising properties are the ability to dramatically enhance water flow through or past the nanostructures. There is much research being conducted to understand how this happens and ultimately how to make best use of this property to potentially purify water, desalinate water, and meet other goals in biomedical and energy research. Challenges remain in how to efficiently manufacture these materials and how to adjust their structures to achieve the best results.

    Thanks to everyone who supported this project.

    See the full article here.


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings
    World Community Grid (WCG) 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.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Microbiome Immunity Project

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

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  • richardmitnick 3:07 pm on June 27, 2018 Permalink | Reply
    Tags: BOINC-Berkeley Open Infrastructure for Network Computing, Help Cure Muscular Dystrophy project,   

    From World Community Grid (WCG): “Data from Help Cure Muscular Dystrophy Project Helps Shed Light on the Mysteries of Protein Interactions” 

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    From World Community Grid (WCG)

    26 Jun 2018
    Dr. Alessandra Carbone
    Sorbonne Université

    Summary
    Protein-protein interactions are the basis of cellular structure and function, and understanding these interactions is key to understanding cell life itself. Dr. Alessandra Carbone and her team continue to analyze data on these interactions from the Help Cure Muscular Dystrophy project, and they recently published a new paper to contribute to the body of knowledge in this field.


    29 mminutes

    Dr. Alessandra Carbone (principal investigator of the Help Cure Muscular Dystrophy project) and team have published a paper entitled “Hidden partners: Using cross-docking calculations to predict binding sites for proteins with multiple interactions” in the journal Proteins.

    Protein interactions are the basis for most biological functions. How they interact with each other and other compounds (such as DNA, RNA, and ligands) in the cell is key to understanding life and disease functions. Complicating things, proteins often interact with more than one other kind of protein. To better understand protein functions, tools are required to uncover these potential interactions.

    Different parts (surfaces) of the protein can be binding sites that attract another protein. This paper describes a methodology the research team developed to better predict these alternative binding sites. A subset of the Help Cure Muscular Dystrophy project data was used to validate their technique, which will be subsequently applied to the whole dataset computed via World Community Grid.

    See the full article here.


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.

    Stem Education Coalition

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings

    World Community Grid (WCG) 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.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Microbiome Immunity Project

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 3:19 pm on June 19, 2018 Permalink | Reply
    Tags: , BOINC-Berkeley Open Infrastructure for Network Computing, ,   

    From World Community Grid (WCG): “Microbiome Immunity Project Researchers Create Ambitious Plans for Data” 

    New WCG Logo

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    From World Community Grid (WCG)

    By: Dr. Tomasz Kościółek and Bryn Taylor
    University of California San Diego
    19 Jun 2018

    Summary
    The Microbiome Immunity Project researchers—from Boston, New York, and San Diego—met in person a few weeks ago to make plans that include a 3D map of the protein universe and other far-ranging uses for the data from the project.


    The research team members pictured above are (from left to right): Vladimir Gligorijevic (Simons Foundation’s Flatiron Institute), Tommi Vatanen (Broad Institute of MIT and Harvard), Tomasz Kosciolek (University of California San Diego), Rob Knight (University of California San Diego), Rich Bonneau (Simons Foundation’s Flatiron Institute), Doug Renfrew (Simons Foundation’s Flatiron Institute), Bryn Taylor (University of California San Diego), Julia Koehler Leman (Simons Foundation’s Flatiron Institute). Visit the project’s Research Participants page for additional team members.

    During the week of May 28, researchers from all Microbiome Immunity Project (MIP) institutions (University of California San Diego, Broad Institute of MIT and Harvard, and the Simons Foundation’s Flatiron Institute) met in San Diego to discuss updates on the project and plan future work.

    Our technical discussions included a complete overview of the practical aspects of the project, including data preparation, pre-processing, grid computations, and post-processing on our machines.

    We were excited to notice that if we keep the current momentum of producing new structures for the project, we will double the universe of known protein structures (compared to the Protein Data Bank) by mid-2019! We also planned how to extract the most useful information from our data, store it effectively for future use, and extend our exploration strategies.

    We outlined three major areas we want to focus on over the next six months.

    Structure-Aided Function Predictions

    We can use the structures of proteins to gain insight into protein function—or what the proteins actually do. Building on research from MIP co-principal investigator Richard Bonneau’s lab, we will extend their state-of-the-art algorithms to predict protein function using structural models generated through MIP. Using this new methodology based on deep learning, akin to the artificial intelligence algorithms of IBM, we hope to see improvements over more simplistic methods and provide interesting examples from the microbiome (e.g., discover new genes creating antibiotic resistance).

    Map of the Protein Universe

    Together we produce hundreds of high-quality protein models every month! To help researchers navigate this ever-growing space, we need to put them into perspective of what we already know about protein structures and create a 3D map of the “protein universe.” This map will illustrate how the MIP has eliminated the “dark matter” from this space one structure at a time. It will also be made available as a resource for other researchers to explore interactively.

    Structural and Functional Landscape of the Human Gut Microbiome

    We want to show what is currently known about the gut microbiome in terms of functional annotations and how our function prediction methods can help us bridge the gap in understanding of gene functions. Specifically, we want to follow up with examples from early childhood microbiome cohorts (relevant to Type-1 diabetes, or T1D) and discuss how our methodology can help us to better understand T1D and inflammatory bowel disease.

    The future of the Microbiome Immunity Project is really exciting, thanks to everyone who makes our research possible. Together we are making meaningful contributions to not one, but many scientific problems!

    See the full article here.


    five-ways-keep-your-child-safe-school-shootings
    Please help promote STEM in your local schools.

    Stem Education Coalition

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings

    World Community Grid (WCG) 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.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    Microbiome Immunity Project

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 8:43 am on May 23, 2018 Permalink | Reply
    Tags: , BOINC-Berkeley Open Infrastructure for Network Computing, , ,   

    From World Community Grid (WCG): “FightAIDS@Home – Phase 2 Prepares for A New Stage” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    By: The FightAIDS@Home research team
    22 May 2018

    Summary
    The FightAIDS@Home – Phase 2 researchers are making plans to write a paper and to test new compounds as part of the continuing search for new and better treatments.

    1
    No image caption or credit.

    Background

    Researchers all over the world have been making advances in the battle against HIV/AIDS for many years. However, AIDS-related complications still affect far too many people. UNAIDS estimates that 36.7 million people were living with HIV in 2016. And while AIDS-related deaths have decreased significantly since their peak in 2005, approximately 1 million people died of causes related to AIDS in 2016. (See the UNAIDS website for more statistics.)

    HIV continues to be a challenge because it quickly mutates in ways that make existing drug treatments ineffective. FightAIDS@Home joined World Community Grid more than a decade ago with the simple but challenging goal of finding new treatments for HIV. During Phase 1 of the project, the team identified thousands of potentially promising candidates to be confirmed experimentally in the lab. However, because it’s cost and time prohibitive to lab test all the potential candidates, Phase 2 was created to prioritize the candidate compounds by evaluating them with more accurate methods.

    Current Work

    Our team is processing the current type of work units through World Community Grid as quickly as possible. Once these work units are completed, we plan to write a paper about the process, including its strengths, limitations, and lessons learned.

    We are also planning to use World Community Grid’s computing power to analyze new compounds that are important to our work with the HIVE Center at the Scripps Research Institute. This work will begin after we run a sample of these new compounds on our own grid computing network.

    Thank You

    We appreciate everyone who continues to donate their computing power to the search for better anti-HIV treatments. We also encourage everyone to opt in to Phase 2 of the project—the more quickly we can run through the current work units, the sooner we can move ahead to new compounds.

    See the full article here.

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings


    five-ways-keep-your-child-safe-school-shootings

    Please help promote STEM in your local schools.
    stem
    Stem Education Coalition

    World Community Grid (WCG) 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.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 1:53 pm on April 29, 2018 Permalink | Reply
    Tags: BOINC-Berkeley Open Infrastructure for Network Computing, Impact of atmospheric aerosols on climate change (Far Eastern Federal University- Russia), Impact of climate change on public health (Emory University USA), Rainfall modeling in Africa (Delft University of Technology- Netherlands),   

    From World Community Grid (WCG): “Announcing Three Winning Climate Change Projects” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    Announcing Three Winning Climate Change Projects

    26 Apr 2018

    Summary
    After a rigorous review of dozens of applications from all over the world, we’re excited to announce the research groups who will receive supercomputing power, weather data, and cloud storage from IBM to accelerate climate change science.

    1

    As our planet faces the mounting impacts of climate change, scientists are on the front lines of understanding complex consequences and developing solutions.

    We’ve heard from climate change scientists that common bottlenecks they face include limited access to weather data, and insufficient computing power and data storage capacity to accurately simulate the impacts of climate change.

    These are some of the reasons why IBM Corporate Citizenship recently invited scientists to apply for grants of massive computing power from World Community Grid, meteorological data from The Weather Company, and data storage from IBM Cloud Object Storage to support their climate change or environmental research projects. (More information about these IBM resources can be found here.)

    As our planet faces the mounting impacts of climate change, scientists are on the front lines of understanding complex consequences and developing solutions. Common bottlenecks facing scientists conducting foundational research include limited access to weather data, and insufficient computing power and data storage capacity to accurately simulate the impacts of climate change.

    To build on IBM’s decades-long commitment to environmental stewardship, IBM Corporate Citizenship is helping overcome these roadblocks by donating technology and data to three foundational climate change research projects.

    Groundbreaking Research Projects

    These IBM resources–crowdsourced computing power through World Community Grid, weather data from The Weather Company, and IBM Cloud Object Storage–will support three groundbreaking new research projects, chosen from over 70 applications for their potential to make a significant contribution to our understanding of climate change impacts and potential solutions.

    Impact of climate change on public health (Emory University, USA)

    This project will examine the impact of climate change on temperature and air pollution at local levels, helping researchers understand the impact of a changing climate on human health.

    Impact of atmospheric aerosols on climate change (Far Eastern Federal University, Russia)

    Atmospheric aerosols, such as dust, smoke and pollution, both absorb and reflect sunlight in the atmosphere, and represent the greatest area of uncertainty in climate science today, according to the UN Intergovernmental Panel on Climate Change (IPCC). This project aims to determine how super-micron particles (6 to 12 micrometers in diameter) interact with sunlight and how they contribute to atmospheric temperatures – information that will improve the accuracy of climate models.

    Rainfall modeling in Africa (Delft University of Technology, Netherlands)

    In Africa, agriculture relies heavily on localized rainfall, which is difficult to predict. In collaboration with the Trans-African Hydro-Meteorological Observatory, researchers will simulate rainfall on the continent – information that could help farmers be more resilient, among other weather and hydrology applications.

    In return for this support, the winning scientists agree to publicly release the data from their collaboration with IBM, enabling the global community to benefit from and build upon their findings.

    Supercharged by IBM Resources

    Each of these three winning projects will use one or more of these resources:
    Crowdsourced computing power

    Scientists receive free, 24/7 access to computing power through World Community Grid, a philanthropic initiative of IBM that enables anyone with a computer or Android device to support scientific research by carrying out virtual research experiments on their devices.

    Through the contributions of over 740,000 individuals and 440 organizations, the initiative has enabled a number of breakthrough discoveries in environmental research by helping scientists discover new materials for efficient solar energy, study the impact of management policies on large watershed areas and uncover more efficient ways to filter water.

    “World Community Grid enabled us to find
    new possibilities for solar cells on a
    timescale that matters to humanity–in other
    words, in a few years instead of decades.”

    Dr. Alan Aspuru-Guzik
    Professor of Chemistry and Chemical Biology
    Harvard University

    Weather data

    The historical and real-time weather data of The Weather Company, an IBM business, can help scientists advance our understanding of environmental systems and support the design of solutions to prevent, mitigate against, and adapt to climate change.

    Cloud storage

    For scientists who work on environmental research initiatives with very large data sets, IBM Cloud Object Storage provides a scalable platform to store and analyze the results of virtual experiments on World Community Grid and conduct further investigations.
    Frequently Asked Questions
    What is World Community Grid?
    We’re a philanthropic initiative of IBM that connects researchers with free and massive computing power, donated by volunteers around the world, to advance scientific research on our planet’s most pressing issues. Anyone with a computer or Android device can sign up to participate. To date, over 740,000 individuals and 430 organizations have contributed over a billion years of computing power to support 29 research projects, including studies about low-cost water filtration systems and new materials for capturing solar energy efficiently.

    Our research partners have published over 50 peer-reviewed scientific papers in journals including Science, Nature and PLOS. This crowdsourced computing power, which is provided to researchers for free, often allows them to take on research efforts at an unprecedented scale, pursue new research approaches and get the work done in years instead of decades.

    How does World Community Grid work?
    Scientists from institutions all over the world come to us with research projects that need massive amounts of computing power. Using their research simulation or modeling software tool of choice, we integrate that software into our platform and distribute millions of virtual research experiments to thousands of World Community Grid volunteers, who perform these calculations on their computers and Android devices. World Community Grid validates and bundles the results of these calculations and sends them back to the researchers. Through World Community Grid, scientists can not only access massive computing power at no cost, but can also engage the public in their research.

    What climate and environmental research has World Community Grid supported to date?

    Since 2004, World Community Grid has supported a number of environmental research efforts including:

    Clean Energy Project – In what is believed to be the largest quantum chemistry experiment ever performed, researchers at Harvard University screened millions of organic photovoltaic compounds to predict their potential for converting sunlight into electricity. Amongst these, 36,000 were predicted to double the efficiency of most carbon-based solar cells currently in production.
    Computing for Clean Water – Researchers at Tsinghua University in Beijing used World Community Grid to simulate the flow of water through carbon nanotubes at an unprecedented level of detail. In doing so, they discovered a phenomenon that points to a new possibility for water filtration which could one day improve access to clean water for the nearly one billion people around the world who lack access to it.

    Computing for Sustainable Water – Scientists at University of Virginia studied the impact of management policies on water quality in the Chesapeake Bay to gain deeper insights into what actions can lead to restoration, health and sustainability of this important water resource.
    Uncovering Genome Mysteries – Researchers examined 200 million genes from a wide variety of life forms, such as microorganisms found on seaweed from Australian coastlines and in the Amazon river. The goal of their work is to augment knowledge about biochemical processes in general, identify how organisms interact with each other and the environment, and document the current baseline microbial diversity, allowing a better understanding of how microorganisms change under environmental stresses, such as climate change.

    What kind of computing power is being made available with the grant?

    Scientists who receive these awards will use World Community Grid, a philanthropic IBM initiative that provides scientists with massive amounts of computing power, for free. Through World Community Grid, computational research calculations are distributed to thousands of volunteers around the world who perform these calculations on their computer or Android devices.

    In addition, we carry out the technical work to integrate the researchers’ computational research tool of choice into the World Community Grid platform. We also provide communications and outreach support to engage and educate the public in this research.

    How is the computing power being made available by World Community Grid different from a supercomputer?
    As one of the researchers who has used World Community Grid for several years once said, “It turns out that having hundreds of thousands of computers in parallel accelerates things more than having a supercomputer.” World Community Grid provides scientists with 24/7 access to enough computing power to match some of the world’s most powerful supercomputers. But unlike a traditional supercomputer, World Community Grid distributes the computational work to thousands of computers worldwide, each of which is provided by a volunteer who chooses to make their device available to conduct scientific calculations. For our research partners, this means not having to wait in line for computing resources as they would with most supercomputers at their own institutions. Instead, they receive free access to massive amounts of computing power, while engaging the public in their research.

    What weather data is being made available to grant recipients?
    Grant recipients have free access to weather data from The Weather Company, an IBM business, to support their research. The data may include global weather forecasts, historical observations, and current weather conditions. Access to the data will be provided through web-based APIs, while the project runs on World Community Grid.

    What cloud storage capabilities are being made available to grantees?
    Grant recipients have free access to IBM Cloud Object Storage for all data storage needs related to their IBM-supported project, while the project runs on World Community Grid. Technical assistance will also be provided to assess their data storage needs and determine appropriate storage solutions.

    What were the criteria for successful proposals?
    Successful proposals met the following criteria:

    Not for profit: conducted by public or nonprofit organizations
    Tackle climate change: Advance understanding of the impacts of climate change, and/or strategies to adapt to or mitigate the impacts of climate change.
    Contribute to open science: all data generated by World Community Grid volunteers must be made freely available to the scientific community.
    Enabled, accelerated or enhanced by the resources we offer: climate or environmental computational studies that require significant computer processing power and can be divided into small independent computations, may need weather data, and/or could benefit from large amounts of cloud-based storage.

    How were applications evaluated?
    A team of IBM scientists and outside scientists with expertise in environmental and climate change science reviewed each application for:

    Scientific merit
    Potential to contribute to the global community’s understanding of specific climate change and/or environmental science challenges
    Capacity of the research team to manage a sustained research project
    Demonstrated need for IBM resources

    What commitment do scientists make in return?
    In return for these free resources, scientists agree to support our open data policy by publicly releasing the research data from their World Community Grid project, to enable the global scientific community to benefit from and build upon their findings. Research teams also agree to engage the volunteers in their research through regular communications through World Community Grid communication channels.

    When will these projects begin running on World Community Grid?
    We have begun the onboarding process for the projects, and are planning to launch the first project later in 2018. We will be posting updates about this process on our website.

    Can researchers still apply for these resources?
    We’re not currently accepting applications that include data from The Weather Company and storage from IBM Cloud, but any researchers who are interested in using World Community Grid’s computing power are welcome to submit an application.

    How do I make sure that I start contributing to these projects as soon as they’re launched?

    If you are already a World Community Grid volunteer, go to the My Projects page, where you can choose to opt in to new projects as they become available.

    If you’re not yet a World Community Grid volunteer, you can sign up to be notified as soon as the first of these three projects is launched. You can also join World Community Grid right now and support our existing projects.

    NOTIFY ME OF PROJECT LAUNCHES

    See the full article here.

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    World Community Grid (WCG) 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.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 9:48 am on April 21, 2018 Permalink | Reply
    Tags: BOINC-Berkeley Open Infrastructure for Network Computing, , , , What's tech got to do with it?   

    From World Community Grid (WCG): “What’s tech got to do with it?” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    We went to SXSW to talk about how volunteer computing can help save the planet.

    20 Apr 2018
    Summary
    World Community was invited to give two presentations on the power of crowdsourced computing power at SXSW 2018 in Austin, Texas. See the full presentations, as well as a short video with excerpts from both, in this article.

    We were thrilled to be invited to give two presentations in the Code and Programming track at SXSW 2018. You can see both presentations in full, as well as a few excerpts in the first video below.

    In this short video, two scientists talk about the crucial issues they’re researching: climate change and clean energy. World Community Grid project manager Juan Hindo and software developer Jonathan Armstrong explain the important role of volunteers in accelerating research.

    Last year, IBM issued a call for proposals to climate change and environmental researchers, offering them not only World Community Grid supercomputing power, but also data from The Weather Company and storage on IBM Cloud Object Storage. In this video, IBM Distinguished Engineer and Chief Scientist Lloyd Treinish joins Juan and Jonathan to talk about the most pressing issues in climate change, the extent of the climate change science community’s technical needs, and the opportunity for the tech community to help.

    Dr. Alan Aspuru-Guzik was the lead researcher for the Clean Energy Project, which uncovered a large number of potential new and improved solar cells. In this presentation, Alan gave an overview of the work so far, and talked about his plans for further extending his collaboration with World Community Grid and other organizations.

    See the full article here.

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    World Community Grid (WCG) 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.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-
    Smash Childhood Cancer4

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
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  • richardmitnick 10:08 am on March 29, 2018 Permalink | Reply
    Tags: , , Bloomberg View, BOINC-Berkeley Open Infrastructure for Network Computing, , ,   

    From Rosetta@home via Bloomberg View: “Protein Engineering May Be the Future of Science” 

    Rosetta@home

    Rosetta@home

    2

    Bloomberg View

    March 27, 2018
    Faye Flam

    Some scientists think designing new proteins could become as significant as tweaking DNA.

    3
    Let’s build a better sperm whale. Photograph: SSPL/Getty Images

    Scientists are increasingly betting their time and effort that the way to control the world is through proteins. Proteins are what makes life animated. They take information encoded in DNA and turn it into intricate three-dimensional structures, many of which act as tiny machines. Proteins work to ferry oxygen through the bloodstream, extract energy from food, fire neurons, and attack invaders. One can think of DNA as working in the service of the proteins, carrying the information on how, when and in what quantities to make them.

    Living things make thousands of different proteins, but soon there could be many more, as scientists are starting to learn to design new ones from scratch with specific purposes in mind. Some are looking to design new proteins for drugs and vaccines, while others are seeking cleaner catalysts for the chemical industry and new materials.

    David Baker, director for the Institute for Protein Design at the University of Washington, compares protein design to the advent of custom tool-making. At some point, proto-humans went beyond merely finding uses for pieces of wood, rock or bone, and started designing tools to suit specific needs — from screwdrivers to sports cars.

    See the full article here.

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    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.

    U Washington Dr. David Baker

    Rosetta screensaver

    BOINC

    My BOINC

     
  • richardmitnick 10:58 am on March 21, 2018 Permalink | Reply
    Tags: , BOINC-Berkeley Open Infrastructure for Network Computing, Drug Search for Leishmaniasis Project Continues Quest for Better Treatments, ,   

    From WCG: “Drug Search for Leishmaniasis Project Continues Quest for Better Treatments” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    20 Mar 2018
    Dr. Carlos Muskus López
    Coordinator, Molecular Biology and Computational Unit, PECET University of Antioquia

    Summary
    The Drug Search for Leishmaniasis researchers recently conducted lab testing on 10 compounds. The testing showed that none of the compounds were good potential treatments, and the researchers will turn their attention to additional compounds.

    1
    Sandflies, such as the P. papatasi shown above, are responsible for the spread of leishmaniasis.

    Short description of the team’s latest findings

    Leishmaniasis is one of the most neglected tropical diseases in the world, infecting more than two million people in 98 countries. The current treatments for all forms of leishmaniasis can cause severe side effects, including death. Furthermore, drug resistant parasites are causing major problems in many countries. For these reasons, there is an urgent need for new, safe, and inexpensive drug compounds.

    The Drug Search for Leishmaniasis team has continued their lab testing since their last update. The most recent round of testing involved 10 compounds that had been identified as having potential to be safer, more effective treatments.

    The compounds were tested first for toxicity, then for effectiveness against two common parasites that can cause leishmaniasis. Based on the testing, none of the compounds tested would be effective treatments for the disease.

    The researchers will make these results public, as they have done with their data to-date. This will alert other scientists to the strong possibility that these particular compounds are not effective against leishmaniasis, and help them make decisions about testing other compounds. Once the team has obtained additional funding, they will test additional compounds that may be useful in treating leishmaniasis.

    Anyone interested in a full scientific description of this latest round of testing can read below. Thanks to everyone who supported this project.

    In vitro evaluation of the anti-leishmanial activity of predicted molecules by docking

    In order to determine if in silico predicted molecules with potential leishmanicidal activity could have the possibility of passing to in vivo assays, the molecules must first pass cytotoxicity testing against human cells in vitro. Then, those molecules that show low or no cytotoxicity are evaluated for parasite growth inhibition in human macrophages and the effective concentration 50 (EC50). The EC50 is the concentration of a molecule that kills 50% of the parasites in vitro.

    Evaluation of Anti-Leishmanial Activity

    Prior to the determination of the effective concentration 50 (EC50), all the compounds were pre-selected, by evaluating the effect on the percentage of infection in intracellular amastigotes in the U-937 cell line compared with amastigotes controls, in the absence of the compound.

    The activity of the compounds was evaluated on intracellular parasites (amastigote stage) obtained after in vitro infection of macrophages. The U-937 cells were infected with fluorescent promastigotes in stationary growth phase in a 30:1 parasite:cell ratio for the Leishmania panamensis UA140 strain and 20:1 for Leishmania braziliensis UA301 strain. The infected cells were exposed different concentration of the compounds for 72 hours (see the concentrations used for each compound, in a note below the Table 2). As infection control, infected cells were used in the absence of the compounds, and amphotericin B was used as a positive control. After 72 hours of incubation, the cells were carefully removed from the bottom of the dish and analyzed in a flow cytometer, reading at 488 nm excitation and 525 nm emission with an Argon4 laser.

    The anti-Leishmania activity was determined based on the parasite load, which is the number of parasites in the infected cells exposed to the concentration selected for each compound or amphotericin B. The decrease in parasite load, called inhibition of infection was calculated using the fluorescence mean intensity values €‹(MFI) and using the following formula: % Infection = [MFI cells infected and exposed to the compound or amphotericin B / MFI infected of unexposed cells] × 100). The MFI values ‹obtained for the infected cells in the absence of drug or compound corresponds to 100% of the infection. In turn, the percentage of inhibition of the infection corresponds to 100% of the infection -% infection in the presence of the compound.

    See the full article here.

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    World Community Grid (WCG) 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.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-
    Smash Childhood Cancer4

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 10:40 am on March 9, 2018 Permalink | Reply
    Tags: , , , BOINC-Berkeley Open Infrastructure for Network Computing, ,   

    From WCG “Microbiome Immunity Project Already Extending the Known Universe of Protein Structures” 

    New WCG Logo

    WCGLarge

    World Community Grid (WCG)

    WCG Microbiome Immunity Project

    7 Mar 2018
    By: Tomasz Kosciolek, PhD
    UC San Diego Center for Microbiome Innovation

    Summary
    The Microbiome Immunity Project is off to a great start on predicting the structures of hundreds of thousands of bacterial proteins within the human gut. Read about their progress and their plans in their first project update.

    Background

    The Microbiome Immunity Project was created to better understand the role of the microbiome in intestinal immune response and diseases such as Type 1 Diabetes (T1D) and Inflammatory Bowel Disease (IBD). In this project, we predict structures of bacterial proteins and use this information to annotate their functions and to understand host-microbiome interactions which are responsible for the pathology of IBD and T1D. This is a massive undertaking, as the human gut microbiome has more than 2 million unique proteins, with hundreds of thousands of proteins potentially interacting with human cells. A project of this scale is only possible thanks to the power of World Community Grid.

    Our Progress So Far

    With your help, we have already predicted the structures of over 50,000 prioritized proteins! In the grand scheme of the 2 million unique bacterial proteins in our gut, this may not seem like a lot, but keep in mind that the experimental work to date covers only approximately 125,000 proteins. In only 6 months we have made tremendous progress by extending our universe of known protein structures by almost 28 percent!

    You may have already realized that at this pace, predicting all bacterial protein structures would take years to complete. Fortunately, we don’t have to predict every single structure, because proteins can be grouped into families. These families consist of proteins with similar structures and functions, enabling a comprehensive understanding of the family’s function with only one representative member per family. Once we identify protein families of interest, we will investigate them in more detail.

    In the meantime, we have adjusted our strategy on how to prioritize the predictions. Instead of looking only at bacterial genomes (genes of an individual bacterial species), we are investigating bacterial pangenomes (genes of all bacterial strains belonging to the same species). We then prioritize those pangenomes according to their prevalence between individuals in cohort studies investigating the role of microbiome in IBD and T1D. This approach enables us to have the most impact early in the project. We not only have thorough information on microbes involved in T1D and IBD specifically, but we have also expanded our knowledge of the microbiome in general.

    We are now extracting information from your predictions, and during the course of the project we plan to make the data available to the public for other exciting research. We are also working on methods to improve predictions of protein functions, enabling us to find the important protein families involved in T1D and IBD among thousands of predictions we have made so far.

    All this progress has been made possible thanks to your generous contributions! There is still a lot to discover about the microbiome, but with each computation that you support we are getting a step closer to having a more detailed picture of this important ecosystem inside each of our bodies and understanding IBD and T1D. So, thank you and let’s continue working together on unraveling the mysteries of microbiome!

    See the full article here.

    Ways to access the blog:
    https://sciencesprings.wordpress.com
    http://facebook.com/sciencesprings

    Please help promote STEM in your local schools.
    STEM Icon

    Stem Education Coalition

    World Community Grid (WCG) 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.”
    WCG projects run on BOINC software from UC Berkeley.
    BOINCLarge

    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.

    BOINC WallPaper

    CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

    My BOINC
    MyBOINC
    “Download and install secure, free software that captures your computer’s spare power when it is on, but idle. You will then be a World Community Grid volunteer. It’s that simple!” You can download the software at either WCG or BOINC.

    Please visit the project pages-
    Smash Childhood Cancer4

    FightAIDS@home Phase II

    FAAH Phase II
    OpenZika

    Rutgers Open Zika

    Help Stop TB
    WCG Help Stop TB
    Outsmart Ebola together

    Outsmart Ebola Together

    Mapping Cancer Markers
    mappingcancermarkers2

    Uncovering Genome Mysteries
    Uncovering Genome Mysteries

    Say No to Schistosoma

    GO Fight Against Malaria

    Drug Search for Leishmaniasis

    Computing for Clean Water

    The Clean Energy Project

    Discovering Dengue Drugs – Together

    Help Cure Muscular Dystrophy

    Help Fight Childhood Cancer

    Help Conquer Cancer

    Human Proteome Folding

    FightAIDS@Home

    faah-1-new-screen-saver

    faah-1-new

    World Community Grid is a social initiative of IBM Corporation
    IBM Corporation
    ibm

    IBM – Smarter Planet
    sp

     
  • richardmitnick 6:52 pm on March 6, 2018 Permalink | Reply
    Tags: , BOINC-Berkeley Open Infrastructure for Network Computing, , , , , U Wasington Medicine News Room   

    From UW Medicine Newsroom: “Scientists create complex transmembrane proteins from scratch” 

    U Washington
    University of Washington

    UW Medicine Newsroom

    March 1, 2018
    Leila Gray
    206.685.0381
    leilag@uw.edu

    The ability to build transmembrane proteins opens the way for custom-designing structures that span living cell membranes and perform new tasks.

    1
    Four computer-designed proteins combine to form a transmembrane tetramer with the top of structure facing the cytoplasm. Institute for Protein Design.

    In the living world, transmembrane proteins are found embedded in the membrane of all cells and cellular organelles. They are essential for them to function normally. For example, many naturally occurring transmembrane proteins act as gateways for the movement of specific substances across a biological membrane. Some transmembrane proteins receive or transmit cell signals. Because of such roles, many drugs are designed to target transmembrane proteins and alter their function.

    Now researcher are looking at designing the transmembrane proteins themselve to perform specific tasks.

    “Our results pave the way for the design of multispan membrane proteins that could mimic proteins found in nature or have entirely novel structure, function and uses,” said David Baker, a University of Washington School of Medicine professor biochemistry and director of the UW Institute of Protein Design who led the project.

    U Washington Dr. David Baker

    David Baker’s Rosetta@home project, a project running on BOINC software from UC Berkeley

    But understanding how transmembrane proteins are put together and how they work has proved challenging. Because they act while embedded within the cellular membrane, transmembrane proteins have proven to be more difficult to study than proteins that operate in the watery solution that make up the cells’ cytoplasm or in the extracellular fluid.

    In the new study, Lu and his coworkers used a computer program, developed in the Baker lab and called Rosetta, that can predict the structure a protein will fold into after it has been synthesized. The architecture of a protein is crucial because a protein’s structure determines its function.

    A protein’s shape forms from complex interactions between the amino acids that make up the protein chain and between the amino acids and the surrounding environment. Ultimately, the protein assumes the shape that best balances out all these factors so that the protein achieves the lowest possible energy state.

    The Rosetta program used by Lu and his colleagues can predict the structure of a protein by taking into account these interactions and calculating the lowest overall energy state. It is not unusual for the program to create tens of thousands of model structures for an amino acid sequence and then identify the ones with lowest energy state. The resulting models have been shown to accurately represent the structure the sequence will likely assume in nature.

    Determining the structure of transmembrane proteins is difficult because portions of transmembrane proteins must pass though the membrane’s interior, which is made of oily fats called lipids.

    In aqueous fluids, amino acid residues that have polar sidechains – components that can have a charge under certain physiological conditions or that participate in hydrogen bonding — tend to be located on the surface of the protein where they can interact with water, which has negatively and positively side charges to its molecule. As a result, polar residues on proteins are called hydrophilic, or “water-loving.”

    Non-polar residues, on the other hand, tend to be found packed within the protein core away from the polar aqueous fluid. Such residues are called hydrophobic or “water-fearing.” As a result, the interaction between the water-loving and water-fearing residues of the protein and the surrounding watery fluids helps drive protein folding and stabilizes the protein’s final structure.

    In membranes, however, protein folding is more complicated because the lipid interior of the membrane is non-polar, that is, it has no separation of electrical charges. This means to be stable the protein must place nonpolar, water-fearing residues on its surface, and pack its polar, water-loving residues inside. Then it must find a way to stabilize its structure by creating bonds between the hydrophilic residues within its core.

    The key to solving the problem, said Lu, was to apply a method developed by Baker lab to design the transmembrane portion so that the polar, hydrophilic residues fit in such a way that enough would form hydrongen bonds– that can tie the protein together from within

    “Putting together these ‘buried hydrogen bond networks’ was like putting together a jig-saw puzzle,” Baker said.

    With this approach, Lu and his colleagues were able to manufacture the designed transmembrane proteins inside bacteria and mammalian cells by using as many as 215 amino acids. The resulting proteins proved to be highly thermally stable and able to correctly orient themselves on the membrane. Like naturally occurring transmembrane proteins, the proteins are multipass, meaning they traverse the membrane several times, and assemble into stable multi-protein complexes, such as dimers, trimers and tetramers.

    “We have shown that it is now possible to accurately design complex, multipass transmembrane proteins that can be expressed in cells. This will make it possible for researchers to design transmembrane proteins with entirely novel structures and functions,” said Lu.

    This work was supported by the Howard Hughes Medical Institute, National Institutes of Health (R01GM063919), the Raymond and Beverly Sackler fellowship, and the National Research Foundation of Korea (NRF- 2016R1A6A3A03007871).

    The research is reported in the March 1 issue of the journal Science. Peilong Lu, a senior fellow in the Baker lab, is the paper’s lead author.

    See the full article here .

    Please help promote STEM in your local schools.

    STEM Icon

    Stem Education Coalition

    About UW Medicine

    UW Medicine is one of the top-rated academic medical systems in the world. With a mission to improve the health of the public, UW Medicine educates the next generation of physicians and scientists, leads one of the world’s largest and most comprehensive biomedical research programs, and provides outstanding care to patients from across the globe.

    The UW School of Medicine, part of the UW Medicine system, leads the internationally recognized, community-based WWAMI Program, serving the states of Washington, Wyoming, Alaska, Montana and Idaho. The school has been ranked No. 1 in the nation in primary-care training for more than 20 years by U.S. News & World Report. It is also second in the nation in federal research grants and contracts with $749.9 million in total revenue (fiscal year 2016) according to the Association of American Medical Colleges.

    UW Medicine has more than 27,000 employees and an annual budget of nearly $5 billion. Also part of the UW Medicine system are Airlift Northwest and the UW Physicians practice group, the largest physician practice plan in the region. UW Medicine shares in the ownership and governance of the Seattle Cancer Care Alliance with Fred Hutchinson Cancer Research Center and Seattle Children’s, and also shares in ownership of Children’s University Medical Group with Seattle Children’s.

    u-washington-campus
    The University of Washington is one of the world’s preeminent public universities. Our impact on individuals, on our region, and on the world is profound — whether we are launching young people into a boundless future or confronting the grand challenges of our time through undaunted research and scholarship. Ranked number 10 in the world in Shanghai Jiao Tong University rankings and educating more than 54,000 students annually, our students and faculty work together to turn ideas into impact and in the process transform lives and our world. For more about our impact on the world, every day.
    So what defines us —the students, faculty and community members at the University of Washington? Above all, it’s our belief in possibility and our unshakable optimism. It’s a connection to others, both near and far. It’s a hunger that pushes us to tackle challenges and pursue progress. It’s the conviction that together we can create a world of good. Join us on the journey.

     
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