From World Community Grid (WCG): “15 Years of Shining a Beacon for Science”

From World Community Grid (WCG)

15 Nov 2019

Summary
To mark World Community Grid’s 15th anniversary, we’re asking you as volunteers, researchers, and supporters to publicly show your support for science on social media, in our forum, and on your own website or blog.

“Basic research is performed without thought of practical ends. It results in general knowledge and understanding of nature and its laws. The general knowledge provides the means of answering a large number of important practical problems, though it may not give a complete specific answer to any one of them.”

Thanks to volunteers, researchers, and supporters of science all over the globe, World Community Grid has been a beacon for scientific research since 2004. What started out as a short-term initiative has grown into a major source of computing power for 30 basic science projects to-date. So far, this has led to breakthrough discoveries for childhood cancer, water filtration, and renewable energy, as well as more than 50 peer-reviewed papers about many smaller discoveries that may one day lead to future breakthroughs.

Future discoveries depend on the basic research of yesterday and today. And basic research projects often uncover knowledge no one expected, and lead to paths that were previously unknown. This past year, World Community Grid’s contribution to advances in basic research included:

Working with the FightAIDS@Home researchers to create a new, more efficient sampling protocol
Helping the Microbiome Immunity Project researchers predict almost 200,000 unique protein structures, which is more than all the experimentally solved protein structures to-date
Providing data to help lay the ground for new tools to analyze protein-protein interactions.

This is only possible because of generous volunteers who donate their unused computing power to research, and scientists who have the unique skills and patience to take on challenging problems that have no obvious answers.

We’re inviting everyone involved with World Community Grid to shine a beacon for science this week to help us celebrate our 15th anniversary. You can do this by:

Creating your own social media posts on your favorite platform (tag us on Twitter or Facebook so we can say thanks, and use the hashtag #Beacon4Science)
Posting your thoughts about being involved in World Community Grid in our forum
Sharing our Facebook post and/or retweeting our tweets on starting on Saturday, November 16
Sending us an email with your thoughts at beacon@worldcommunitygrid.org

Feel free to include pictures or videos, especially if they’re science or World Community Grid-related.

Thanks for helping us shine a beacon for science since 2004, and we look forward to continuing our important work together.

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.

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.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

My BOINC

“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

OpenZika

Help Stop TB

Outsmart Ebola together

Mapping Cancer Markers

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

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

IBM – Smarter Planet

From World Community Grid (WCG): “A Graduation, a Paper, and a Continuing Search for the ‘Help Stop TB’ Researchers”

From World Community Grid (WCG)

By: Dr. Anna Croft
University of Nottingham, UK
28 Sep 2018

Summary
In this update, principal investigator Dr. Anna Croft shares two recent milestones for the Help Stop TB research team, and discusses their continuing search for additional researchers.

The Help Stop TB (HSTB) project uses the massive computing power of World Community Grid to examine part of the coating of Mycobacterium tuberculosis, the bacterium that causes tuberculosis. We hope that by learning more about the mycolic acids that are part of this coating, we can contribute to the search for better treatments for tuberculosis, which is one of the world’s deadliest diseases.

Graduation Ceremony for Dr. Athina Meletiou

In recent news for the HSTB project, Dr. Athina Meletiou has now officially graduated. It was a lovely day, finished off with some Pimms and Lemonade in the British tradition.

Athina (center) with supervisors Christof (left) and Anna (right)

Athina and her scientific “body-guard,” Christof

Search for New Team Members Continues

We are still looking for suitably qualified chemists, biochemists, mathematicians, engineers and computer scientists to join our team, especially to develop the new analytical approaches (including machine-learning approaches) to understand the substantial data generated by the World Community Grid volunteers.

We will be talking to students from our BBSRC-funded doctoral training scheme in the next few days and encouraging them to join the project. Click here for more details.

Paper Published

Dr. Wilma Groenwald, one of the founding researchers for the HSTB project, recently published a paper describing some of the precursor work to the project. The paper, which discusses the folding behavior of mycolic acids, is now freely available on ChemRXiv Revealing Solvent-Dependent Folding Behavior of Mycolic Acids from Mycobacterium Tuberculosis by Advanced Simulation Analysis.

We hope to have Athina’s first papers with World Community Grid data available later in the year, and will keep you updated.

Thank you to all volunteers for your support.

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.

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.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

My BOINC

“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

OpenZika

Help Stop TB

Outsmart Ebola together

Mapping Cancer Markers

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

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

IBM – Smarter Planet

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

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.

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 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.

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.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

My BOINC

“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 Cancer

FightAIDS@home Phase II

OpenZika

Help Stop TB

Outsmart Ebola together

Mapping Cancer Markers

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

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

IBM – Smarter Planet

From WCG: “Supercharging Environmental and Climate Change Research”

World Community Grid (WCG)

10 Jul 2017 {Just popped up in social media.]

Summary
IBM invites scientists to apply for grants of supercomputing power through World Community Grid, meteorological data from The Weather Company, and IBM Cloud storage to support their environmental and climate change research projects.

World Community Grid supports research that tackles our planet’s most pressing challenges, including environmental issues. That’s why we’re pleased to announce a new partnership with The Weather Company (an IBM business) and IBM Cloud to provide free technology and data for environmental and climate change projects.

Environmental scientists have long been warning the public about the effects of climate change, and many researchers attribute events such as this summer’s record temperatures in western Europe and the worst drought since the 1940s in parts of Africa to climate change caused by humankind’s activities. The future consequences of climate change could include rising sea levels, potential crop loss, and harsh economic consequences throughout the world. And as funding for scientific research shrinks in many countries, the gap between what scientists must discover–how to mitigate or adapt to climate change–and their resources for such discovery is growing ever wider.

Thanks to the contributions of volunteers all over the globe, World Community Grid is ready to address that gap. Since 2004, our research partners have completed the equivalent of thousands of years of work in just a few years, including enabling advances in environmental science.

For example, scientists at Harvard University used World Community Grid to run the Clean Energy Project [see below], the world’s largest quantum chemistry experiment with the goal of identifying new materials for solar energy. In just a few years, they analyzed millions of chemical compounds to predict their efficiency at converting sunlight into electricity. Their discovery of thousands of promising compounds could advance the development of cheap, flexible solar cell materials that we hope will be used worldwide to reduce carbon emissions and contribute to the fight against climate change.

Other environmental research projects conducted with help from World Community Grid have included new water filtration technology [see below], watershed preservation and crop sustainability.

That’s why we’re pleased to announce that IBM is inviting scientists around the world to apply for grants of supercomputing power from World Community Grid, meteorological data from The Weather Company, and IBM Cloud storage to support their climate change or environmental research projects. Up to five of the most promising environmental and climate-related research projects will be supported. This support, technology, and data can support many potential areas of inquiry, such as impacts on fresh water resources, predicting migration patterns, and developing models to improve crop resilience.

Proposals for projects will be evaluated for scientific merit, potential to contribute to the global community’s understanding of specific climate and environmental challenges and development of effective strategies to mitigate them, and the capacity of the research team to manage a sustained research project. And like all other World Community Grid projects, researchers who receive these resources must agree to abide by our open data policy by publicly releasing the data from their collaboration with us.

Scientists from around the world can apply at http://climate.worldcommunitygrid.org, with a first round deadline of September 15.

There’s still time to mitigate or adapt to the effects of climate change, and scientific research will continue to play a crucial role in how our planet addresses this crisis. We hope you will join us by giving your computers the ability to work around the clock for science.

Scientists Apply Here.

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 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.

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.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

My BOINC

“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

OpenZika

Help Stop TB

Outsmart Ebola together

Mapping Cancer Markers

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

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

IBM – Smarter Planet

From Digital Trends via WCG: “Lend researchers computing power and they’ll use it to study your microbiome”

World Community Grid (WCG)

Digital Trends

No image caption or credit

Conducting millions of experiments in the name of science takes a lot of processing power, but little old you can actually contribute.

Who better to study what lives inside you than, well, you? IBM certainly agrees, and now, the company has teamed up with the Broad Institute of the Massachusetts Institute of Technology (MIT) and Harvard, Massachusetts General Hospital, the University of California San Diego, and the Flatiron Institute to form the Microbiome Immunity Project. It’s described as an IBM-facilitated citizen science project that will take advantage of the “surplus processing power on volunteers’ computers to conduct millions of virtual experiments on behalf of the researchers.” The goal? To map the three million bacterial genes found in your microbiome — which is to say, the bacteria that lives in and on you.

The hope is that this collective science experiment will help scientists gain a deeper understanding of the microbiome’s interaction with our own biochemistry, and thereby examine how these interactions could affect certain diseases, including Type 1 diabetes, Crohn’s disease, and ulcerative colitis. These afflictions already plague hundreds of millions of individuals around the world, but a microbiome study holds out the hope of improved treatment and possibly prevention, of these diseases.

So why haven’t these studies been done before? The problem with conducting this experiment on your own (or on anyone’s own), is that it would require massive supercomputing processing power. And while a single supercomputer might have trouble dealing with so much data, a whole lot of normal computers could do the trick. As such, IBM is actually crowdsourcing computing power by way of IBM’s World Community Grid.

“This type of research on the human microbiome, on this scale, has not been done before,” said Dr. Ramnik Xavier, Institute member and co-director of the infectious disease and microbiome program. “It’s only possible with massive computational power.”

To participate, you need only to download a secure software program [BOINC]that will automatically sense when your computer can offer spare processing power. In those times, IBM will tap your machine to run virtual experiments on behalf of the scientists. The data that comes out of these millions of experiments from across the country will ultimately be analyzed by the project’s team. And in keeping with the crowdsourcing theme, this data will be made publicly available to other scientists, hopefully improving our capacity to treat autoimmune diseases.

As Dr. Rob Knight, Director of the Center for Microbiome Innovation at UC San Diego noted, “By harnessing the efforts of volunteers, we can do something that exceeds the scale of what we have access to by a factor of thousands. For the first time, we’re bringing a comprehensive structural biology picture to the whole microbiome, rather than solving structures one at a time in a piecemeal fashion.”

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 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.

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.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

My BOINC

“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

OpenZika

Help Stop TB

Outsmart Ebola together

Mapping Cancer Markers

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

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

IBM – Smarter Planet

From WCG: “New Lab at Tsinghua University Created to Work on Computing for Clean Water Project Findings”

World Community Grid (WCG)

25 Jul 2017
The Computing for Clean Water team

Summary
Dr. Ming Ma, one of the original members of the Computing for Clean Water research team, has created his own lab at Tsinghua University. Dr. Ma and his team continue to analyze the data generated by the project. Learn more about their current work and plans for the future in this update.

Background

The Computing for Clean Water project was created to provide deeper insight on the molecular scale flow of water through a novel class of filter materials. Thanks to the millions of virtual experiments that the team was able to run on World Community Grid, they discovered conditions under which water can pass through tiny carbon nanotubes much more efficiently. This groundbreaking understanding of a fundamental physical process could help improve access to clean water for millions of people through more efficient water filtration and desalination, and also may have applications in clean energy and medicine.

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

A Growing Team

It has been one year since the main team member, Dr. Ming Ma, returned to Tsinghua University, China, after doing research at University College London and Tel Aviv University. During the past year, as an Associate Professor in the Department of Mechanical Engineering, Dr. Ma recruited four new researchers as members of the team with the help from Prof. Quanshui Zheng, the leader of the Computing for Clean Water team. The new team members include one postdoc, Dr. Wei Cao; and three PhD students: Jin Wang, Kunqi Wang, and Yao Cheng.

Next Steps

The team is now working on two main tasks. The first task is to improve the algorithm used in the previous study (see the reference below) by incorporating new techniques developed during the last three years, and to implement them into LAMMPS, a molecular dynamics software. The second task is to investigate new systems with the algorithm being developed. With these tasks finished, the team wishes to bring new, interesting information into the volunteer computing community.

We thank everyone who supported Computing for Clean Water, and hope to work with you again in the near future.

Reference

M. Ma, F. Grey, L.M. Shen, M. Urbakh, S. Wu, J.Z. Liu, Y.L. Liu, Q.S. Zheng, Water transport inside carbon nanotubes mediated by phonon-induced oscillating friction, Nature Nanotech., 10 (2015) 692-695

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 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.

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.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

My BOINC

“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

OpenZika

Help Stop TB

Outsmart Ebola together

Mapping Cancer Markers

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

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

IBM – Smarter Planet

From FAAH at WCG: “FightAIDS@Home Targeting a Key HIV Protein”

FightAIDS@home

By: The FightAIDS@Home research team
15 Jun 2017

Summary
FightAIDS@Home researchers restarted the first phase of the project at the end of 2016, and in just a few months, they have completed approximately 46 percent of their projected work on World Community Grid. Read about their progress on finding compounds that could stop HIV from replicating.

Background

FightAIDS@Home is searching for possible compounds to target the protein shell of HIV (called a capsid), which protects the virus. Currently, there are no approved drugs that target this protein shell.

The virtual docking techniques used in Phase 1 are an approximation of the potential effectiveness of promising compounds. Phase 2 of FightAIDS@Home uses a different simulation method to double-check and further refine the virtual screening results that are generated in Phase 1.

The research team is examining a library of approximately 1.6 million commercially available compounds to find promising treatment prospects. The team estimates that they will need to carry out roughly 621 million docking computations on World Community Grid to thoroughly test each potential compound. With the help of many volunteers who are supporting this project, they’ve already completed 46 percent of their goal.

You can keep up with the research team’s progress on their website, which includes frequent updates on their experiments and progress.

Please read below for a detailed look at the technical aspects of their recent work.

Insilico search for novel drugs targeting the HIV-1 mature capsid protein

The importance of the capsid protein

The capsid protein (CA) plays crucial roles in the HIV replication cycle1. After viral and host cell membrane fusion, the capsid core is released into the cytoplasm. This core, which corresponds to the assembly of ~1200 capsid proteins, contains and protects viral RNA and proteins from degradation. Reverse transcription occurs in the core in a process which is tightly connected to the capsid core disassembly. This leads to the import of the cDNA viral genome into the host cell’s nucleus, where it is integrated into the host DNA to finalize the infection.

To date, no drugs targeting CA are approved for clinical use. With the goal of identifying novel active molecules which destabilize the capsid core, we set up a high throughput virtual screening (VS) campaign in collaboration with World Community Grid as part of the FightAIDS@Home (FA@H) project.

Figure 1: PDB 4xfx, the hexamer structure of the native HIV-1 mature capsid protein. (Credit: Pierrick Craveur)

Targeted structures

The main target of the docking calculations was the recently solved structure of the CA hexameric assembly2. Four pockets of interest were selected at the surface of the hexamer in order to perform focused dockings, mainly at the CA-CA dimer interfaces. Structural variability surrounding these pockets was analyzed by comparing this X-ray structure from the PDB (4xfx, see Figure 1), and the two full capsid core models assembled by Schulten’s lab3 (3j3q and 3j3y, see Figure 2). Based on that, 36 different conformations were selected as targets for the VS, including the X-ray structure and structures from the models. Each target was set as full rigid and also with a specific combination of residue side chains defined as flexible.

Figure 2: The 2 models of the capsid core assembly. (Credit: Pierrick Craveur)

An extended library of ~1.6 million commercially available compounds was used for the screening. Replicate computations were performed for each docking experiment in order to assess the consistency of the results. In total ~621 million docking computations will be performed on World Community Grid. For the time being, ~46% of the computation is completed, with an ending date estimated at the end of 2017 if the computation does not increase in speed. However, in one month we will be able to propose to our collaborators from the HIVE Center a selection of compounds (focusing one of the four pockets) for experimental binding and infectivity assays.

Other information

Dedicated web pages (see http://fightaidsathome.scripps.edu/Capsid/index.html) were developed to inform the public and the World Community Grid volunteers as the project advances. The pages contain an overview of the project, details on targets and the selection process, a description of the compound library, an hourly updated status of the computations, and a “people” section where volunteers can appear in the page to be fully part of the project.

An automatic pipeline has been developed in order to constantly post-process the docking results received from World Community Grid. These post computations involve the High Performance Computing (HPC) cluster from The Scripps Research Institute, and are mainly related to the identification of the interactions between drug candidates and the CA protein. The pipeline ends in filling a MySQL database, which will be made public as soon as it will be stable. In details, 3.3TB of compressed data are estimated to be received from World Community Grid, and 1TB to be generated after post-processing.

Our team from The Scripps Research Institute of San Diego, which includes Dr. Pierrick Craveur, Dr. Stefano Forli, and Prof. Arthur Olson, really appreciates the essential support this project receives from World Community Grid volunteers around the globe.

References [Sorry, no links]

Campbell, E. M. & Hope, T. J. HIV-1 capsid: the multifaceted key player in HIV-1 infection. Nat Rev Microbiol 13, 471-483, doi:10.1038/nrmicro3503 (2015).
PDB 4xfx : Gres AT, Kirby KA, KewalRamani VN, Tanner JJ, Pornillos O, Sarafianos SG. X-Ray Structures of Native HIV-1 Capsid Protein Reveal Conformational Variability. Science (New York, NY). 2015;349(6243):99-103.
PDB 3j3q & 3j3y : Zhao G, Perilla JR, Yufenyuy EL, et al. Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Nature. 2013;497(7451):643-646.

See the full article here.

Please help promote STEM in your local schools.

Stem Education Coalition

FightAIDS@Home is a project run by the Olson Laboratory that uses distributed computing to contribute your computer’s idle resources to accelerate research into new drug therapies for HIV, the virus that causes AIDS. FightAIDS@Home made history in September 2000 when it became the first biomedical Internet-based grid computing project. FightAIDS@Home was started with Scott Kurowski, founder of Entropia. People all around the World continue to donate their home computer’s idle cycles to running our AutoDock software on HIV-1 protease inhibitor docking problems. With the generous assistance of IBM, we joined World Community Grid in late 2005, and launched FightAIDS@Home on World Community Grid on 21 November, 2005.

How do I join the FightAIDS@Home Project?

All you need to do is download and install the free client software. Once you have done this, your computer is then automatically put to work and you can continue using your computer as usual.

From Help Cure Muscular Dystrophy at WCG: “Help Cure Muscular Dystrophy Lead Researcher Releases Two New Open Data Tools’

World Community Grid (WCG)

29 Jun 2017

Summary
In this letter to volunteers, Dr. Alessandra Carbone, the principal investigator for the Help Cure Muscular Dystrophy project, announces the release of two new open access tools which can accelerate the work of researchers who investigate protein interactions.

The image above is a rendering of a protein structure with three interaction binding sites (in the center, blue/orange/yellow) and its potential partners. Circles represent the level of binding affinity of the protein complexes. The figure illustrates the complexity of the general problem of “protein partners identification” treated in the Help Cure Muscular Dystrophy – Phase 2 project, where potential partners need to be identified and selected within a very large space of interactions.

Dear volunteers for the Help Cure Muscular Dystrophy (Phase 2) project,

I am writing to update you on the analysis of the dataset of docking conformations produced by the Help Cure Muscular Dystrophy (HCMD2) project. The project’s goal was to investigate protein-protein interactions for more than 2,200 proteins whose structures are known, with a particular focus on those proteins that play a role in neuromuscular diseases.

The complete cross-docking dataset containing these protein-protein interactions is under analysis. For this, we are using the various computational tools that we developed in parallel with the calculations run on World Community Grid.

JET2 Viewer: A Repository of Protein Interfaces

We have built a database of protein interfaces for the scientific community. This database, called JET2, is a milestone for the identification of protein partners. Why is this important? The analysis of the HCMD1 and HCMD2 data highlights that a precise description of protein interfaces is crucial in discriminating protein partners, and the database produces a highly accurate set of such predictions. Improvement is still necessary, but the results are already very accurate.

We are now concentrating on extracting useful information relating to muscular dystrophy from the JET2 dataset that your support helped to construct. As you know, progress in research is slow, but we are making definite advances and expect that the methodological approach used in HCMD2 will be very successful in the large-scale identification of protein partners at protein-residue-level resolution! (A protein-residue is a portion of a protein.*)

BIS2Analyzer: A Server to Help Our Data Analysis

We have released a server, called BIS2Analyzer, to help identify signals of interaction based on coevolution analysis within proteins or between protein partners. This server, which is also openly accessible to the scientific community, is important because it can help to identify signals of protein interaction. It was useful to reconstruct the first protein-protein interaction network for viruses (see the reference below on the reconstruction of the network for the Hepatitis C Virus).

Thanking you again strongly for your contributions. I shall keep you updated on our results. Be assured that we are making progress, thanks to your support!

Best regards,

Alessandra

JET2Viewer:

H. Ripoche, E. Laine, N. Ceres, A. Carbone. JET2 Viewer: a database of predicted multiple, possibly overlapping, protein-protein interaction sites for PDB structures, Nucleic Acids Research (2016) doi: 10.1093/nar/gkw1053
E.Laine, A.Carbone. The local geometry and evolutionary conservation of protein surfaces reveal the multiple recognition patches in protein-protein interactions, PLoS Computational Biology, 11(12), e1004580, 2015.

BIS2Analyzer:

F. Oteri, F. Nadalin, R. Champeimont, A. Carbone, BIS2Analyzer: a server for co-evolution analysis of conserved protein families, Nucleic Acids Research, 2017.
R. Champeimont, E. Laine, S.-W. Hu, F. Penin, A. Carbone, Coevolution analysis of Hepatitis C virus genome to identify the structural and functional dependency network of viral proteins, Scientific Reports, Nature Publishing Group, 6:26401, 2016.

*Note: ”Residue-level” means that we not only identify whether protein P is partner of protein Q (yes/no answer), but in which position they interact—identifying which residue of protein P likely interacts with which residue of protein Q.

See the full article here.

Ways to access the blog:
https://sciencesprings.wordpress.com
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Please help promote STEM in your local schools.

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.

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.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

My BOINC

“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

OpenZika

Help Stop TB

Outsmart Ebola together

Mapping Cancer Markers

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

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

IBM – Smarter Planet

From Scripps: “Scientists Jump Hurdle in HIV Vaccine Design”

Scripps Research Institute

June 19, 2017 issue
Madeline McCurry-Schmidt

The new study shows the structure of an important HIV protein, called the envelope glycoprotein, on a common strain of the virus. (Image courtesy Javier Guenaga.)

Scientists at The Scripps Research Institute (TSRI) have made another important advance in HIV vaccine design. The development was possible thanks to previous studies at TSRI showing the structures of a protein on HIV’s surface, called the envelope glycoprotein. The scientists used these structures to design a mimic of the viral protein from a different HIV subtype, subtype C, which is responsible for the majority of infections worldwide.

The new immunogen is now part of a growing library of TSRI-designed immunogens that could one day be combined in a vaccine to combat many strains of HIV.

“All of this research is going toward finding combinations of immunogens to aid in protecting people against HIV infection,” said TSRI Professor Ian Wilson, Hanson Professor of Structural Biology and chair of the Department of Integrative Structural and Computational Biology at TSRI.

The research, published recently in the journal Immunity, was led by Wilson and TSRI Professor of Immunology Richard Wyatt, who also serves as Director of Viral Immunology for the International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center at TSRI.

The new study was published alongside a second study in Immunity, led by scientists at the Karolinska Institute in Stockholm, which showed that the vaccine candidate developed in the TSRI-led study can elicit neutralizing antibodies in non-human primates.

“Together, the two studies reiterate how structure-based immunogen design can advance vaccine development,” said Wyatt.

Solving the Clade C Structure

HIV mutates rapidly, so there are countless strains of HIV circulating around the world. Of these strains, scientists tend to focus on the most common threats, called clades A, B and C.

Like a flu vaccine, an effective HIV vaccine needs to protect against multiple strains, so researchers are designing a set of immunogens that can be given sequentially or as a cocktail to people so their immune systems can prepare for whatever strain they come up against.

In 2013, TSRI scientists, led by Wilson and TSRI Associate Professor Andrew Ward, determined the structure of a clade A envelope glycoprotein, which recognizes host cells and contains the machinery that HIV uses to fuse with cells. Because this is the only antibody target on the surface of HIV, an effective HIV vaccine will have to trigger the body to produce antibodies to neutralize the virus by blocking these activities.

Building on the previous original research, the scientists in the new study set out to solve the structure of the clade C glycoprotein and enable the immune system to fight clade C viruses.

“Clade C is the most common subtype of HIV in sub-Saharan Africa and India,” explained study co-first author Javier Guenaga, an IAVI collaborator working at TSRI. “Clade C HIV strains are responsible for the majority of infections worldwide.”

The scientists faced a big challenge: the clade C envelope glycoprotein is notoriously unstable, and the molecules are prone to falling apart.

Guenaga needed the molecules to stay together as a trimer so his co-author Fernando Garces could get a clear image of the clade C glycoprotein’s trimeric structure. To solve this problem, Guenaga re-engineered the glycoprotein and strengthened the interactions between the molecules. “We reinforced the structure to get the soluble molecule to assemble as it is on the viral surface,” Guenaga said.

The project took patience, but it paid off. “Despite all the engineering employed to produce a stable clade C protein, these crystals (of clade C protein) were grown in very challenging conditions at 4 degrees Celsius and it took the diffraction of multiple crystals to generate a complete dataset, as they showed high sensitivity to radiation damage,” said Garces. “Altogether, this highlights the tremendous effort made by the team in order to make available the molecular architecture of this very important immunogen.”

With these efforts, the glycoprotein could then stay together in solution the same way it remains together on the virus itself. The researchers then captured a high-resolution image of the glycoprotein using a technique called x-ray crystallography.

The researchers finally had a map of the clade C glycoprotein.

Vaccine Candidate Shows Promise

In a companion study, the scientists worked with a team at the Karolinska Institute to test an immunogen based on Guenaga’s findings. The immunogen was engineered to appear on the surface of a large molecule called a liposome—creating a sort of viral mimic, like a mugshot of the virus.

This vaccine candidate indeed prompted the immune system to produce antibodies that neutralized the corresponding clade C HIV strain when tested in non-human primates.

“That was great to see,” said Guenaga. “This study showed that the immunogens we made are not artificial molecules—these are actually relevant for protecting against HIV in the real world.”

In addition to Wyatt, Wilson and Guenaga, the study, “Glycine substitution at helix-to-coil transitions facilitates the structural determination of a stabilized subtype C HIV envelope glycoprotein,” included co-first author Fernando Garces, Natalia de Val, Viktoriya Dubrovskaya and Brett Higgins of TSRI; Robyn L. Stanfield of TSRI and IAVI; Barbara Carrette of IAVI; and Andrew Ward of TSRI, IAVI and the Center for HIV/AIDS Vaccine Immunology & Immunogen Discovery (CHAVI-ID) at TSRI.

This work was supported by the IAVI Neutralizing Antibody Center and Collaboration for AIDS Vaccine Discovery (CAVD; grants OPP1084519 and OPP1115782), CHAVI-ID (grant UM1 AI00663) and the National Institutes of Health (grants P01 HIVRAD AI104722, R56 AI084817 and U54 GM094586).

See the full article here .

YOU CAN HELP IN THE FIGHT AGAINST HIV/AIDS FROM THE COMFORT OF YOUR EASY CHAIR.

The Fight AIDS at home (FAAH@home) Phase II project is now running at World Community Grid (WCG) From Scripps Research Institute.

WCG runs on your home computer or tablet on software from Berkeley Open Infrastructure for Network Computing [BOINC]. Many other scientific projects run on BOINC software.Visit WCG or BOINC, download and install the software, then at WCG attach to the FAAH@home Phase II project. You will be joining tens of thousands of other “crunchers” processing computational data and saving the scientists literally thousands of hours of work at no real cost to you.

My BOINC

Please help promote STEM in your local schools.

Stem Education Coalition

The Scripps Research Institute (TSRI), one of the world’s largest, private, non-profit research organizations, stands at the forefront of basic biomedical science, a vital segment of medical research that seeks to comprehend the most fundamental processes of life. Over the last decades, the institute has established a lengthy track record of major contributions to the betterment of health and the human condition.

The institute — which is located on campuses in La Jolla, California, and Jupiter, Florida — has become internationally recognized for its research into immunology, molecular and cellular biology, chemistry, neurosciences, autoimmune diseases, cardiovascular diseases, virology, and synthetic vaccine development. Particularly significant is the institute’s study of the basic structure and design of biological molecules; in this arena TSRI is among a handful of the world’s leading centers.

The institute’s educational programs are also first rate. TSRI’s Graduate Program is consistently ranked among the best in the nation in its fields of biology and chemistry.

From NC State via WCG: Women in STEM: “Leadership in Public Science: Meet Caren Cooper” Revised and Improved

North Carolina State University

Presented by World Community Grid

June 7, 2017
Matt Shipman

This is one in a series of five Q&As with the members of NC State’s Leadership in Public Science faculty cluster. Read more about the cluster.

Caren Cooper wrote the book on citizen science. Literally. That made her a natural fit for NC State’s Leadership in Public Science effort.

Cooper is an ecologist whose work involves collaborating with bird lovers to learn more about wildlife and ecosystems in urban, suburban and rural environments. She is assistant head of the biodiversity research lab at the North Carolina Museum of Natural Sciences and a research associate professor in NC State’s Department of Forestry and Environmental Resources. She came to Raleigh from the Cornell Lab of Ornithology, but it was a bit of a homecoming; Cooper got her undergrad degree at NC State.

As for her book, citizen science is right there in the title: Citizen Science: How Ordinary People Are Changing the Face of Discovery. You can also see Cooper talk about citizen science and its relationship to public science by checking out her TEDx talk online.

Caren Cooper

Learn about what Cooper is working on.

What does your research focus on?

I’m interested in a variety of natural processes and human behaviors related to environmental change. I value and use citizen science approaches to investigate natural-human systems and map environmental changes and disparities. I enjoy exploring the potential of citizen science to manage natural resources and to bring varied hobby groups into citizen science, like birders, nest box monitors, duck hunters, pigeon fanciers, etc.

What does “public science” mean to you, and how does it factor into your work?

To me, public science refers to science that is transparent, out in the open and accessible to all. I think of citizen science as networks of volunteers helping to advance knowledge and public scientists as professionals building and tending those networks and helping people make meaning of the collective information.

I think successful public scientists must be familiar with the teamwork of designing and implementing citizen science, public communication of science in many forms and open science practices from the start of a research project to its completion and again with the next iteration. Citizen science often looks like it is simply people volunteering in service to science, but in a public science context, it is really about bridging the gap between science and society to make sure that science is in service to humanity.

What drew you to public science in the first place?

When I became a scientist, I liked to do all parts of scientific research myself. That’s how I defined being a scientist: someone who can carry out research independently. My husband and I started a family while I was pursing my Ph.D. Field work became difficult, and my priorities shifted.

I was drawn to citizen science at first because it was a way for birdwatchers to collect all the data that I would ever need. Unexpectedly, it also sparked my interest in the social sciences, science communication and open science. I found it puzzling as to why scientists regarded citizen science poorly and typically failed to recognize its many contributions.

At first I was bothered by the lack of acknowledging lay expertise and the efforts and abilities of volunteers. Then I became bothered by the lack of acknowledging the limits of scientific inquiry — there are some big questions that scientists can’t answer by working alone. Citizen science is a social movement among volunteers within science, which I find fascinating and exciting. Public science is a movement among professionals to support citizen science and other forms of public engagement in science, while also supporting the engagement of scientists with the public and in the public sphere.

What sort of public science projects are you working on at NC State?

I’m helping develop SciStarter.com as a central hub for people to find and participate in citizen science projects around the world. We are also designing SciStarter with tools to help projects become more sustainable by sharing resources related to recruitment, retention and communication with volunteer communities. With SciStarter, we will also help advance understanding of the design and outcomes of citizen science.

I run a citizen science project called Sparrow Swap, which partners with volunteers who monitor nest boxes and view house sparrows as a pest species. They collect house sparrow eggs according to one of four protocol options and donate those eggs to the collections at the NC Museum of Natural Sciences, where my lab is based. We use the eggs to study geographic variation in eggshell patterns and color, and to determine whether eggshells can be used as a biological tool for identifying and mapping environmental contaminants. Volunteers also collect data on the effectiveness of different management options, including swapping in egg replicas (which we paint at the museum) for real eggs and hopefully reducing house sparrow reproduction and their disturbance of native nesting birds. We are developing an online interactive guide to the basics of wildlife management principles.

We are soon launching Sound Around Town in partnership with other universities to support soundscape studies led by the National Park Service (NPS). In Sound Around Town, volunteers will be able to borrow sound recording equipment from their local library and deploy the equipment in their backyards to provide soundscape data to the NPS. They will also use our listening app to ground-truth the recordings and provide information on their feelings and perceptions of each type of sound they identify. Though the equipment loans through libraries will be available only in select cities, we hope volunteers across the country will use the listening app in many urban and residential soundscapes. I’m interested in disparities among communities in noise pollution, which is a combination of actual soundscapes and perceptions of sounds.

We are also starting to explore the potential of a citizen science project related to finding feather-degrading bacteria.

As a public science cluster, in collaboration with the libraries, we want to make NC State a citizen science campus in which students campuswide have abundant opportunities to do citizen science as part of their campus life.

See the full article here .

Please help promote STEM in your local schools.

Stem Education Coalition

NC State was founded with a purpose: to create economic, societal and intellectual prosperity for the people of North Carolina and the country. We began as a land-grant institution teaching the agricultural and mechanical arts. Today, we’re a pre-eminent research enterprise that excels in science, technology, engineering, math, design, the humanities and social sciences, textiles and veterinary medicine.

NC State students, faculty and staff take problems in hand and work with industry, government and nonprofit partners to solve them. Our 34,000-plus high-performing students apply what they learn in the real world by conducting research, working in internships and co-ops, and performing acts of world-changing service. That experiential education ensures they leave here ready to lead the workforce, confident in the knowledge that NC State consistently rates as one of the best values in higher education.

“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.

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.

CAN ONE PERSON MAKE A DIFFERENCE? YOU BET!!

My BOINC

“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

OpenZika

Help Stop TB

Outsmart Ebola together

Mapping Cancer Markers

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

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

IBM – Smarter Planet