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CMS@Home disruption, Monday 22nd July

I've had the following notice from CERN/CMS IT: >> following the hypervisor reboot campaign, as announced by CERN IT here: https://cern.service-now.com/service-portal/view-outage.do?n=OTG0051185 >> the following VMs - under the CMS Production openstack project - will be rebooted on Monday July 22 (starting at 8:30am CERN time): ... >> | vocms0267 | cern-geneva-b | cms-home to which I replied: > Thanks, Alan. vocms0267 runs the CMS@Home campaign. Should I warn the volunteers of the disruption, or will it be mainly transparent? and received this reply: Running jobs will fail because they won't be able to connect to the schedd condor_shadow process. So this will be the visible impact on the users. There will be also a short time window (until I get the agent restarted) where there will be no jobs pending in the condor pool. So it might be worth it giving the users a heads up. So, my recommendation is that you set "No New Tasks" for CMS@Home sometime Sunday afternoon, to let tasks complete before the 0830 CST restart. I'll let you know as soon as Alan informs me that vocm0267 is up and running again

By lhc@home_classic at 2019-07-17

The Audacious Project

As you may have heard, the [Link] Institute for Protein Design was recently selected as part of [Link] The Audacious Project. This large-scale philanthropic collaboration, which is the successor to the TED Prize, surfaces and funds projects with the potential to change the world. As a result, we are expanding our Seattle-based team of scientists and engineers who will work together to advance Rosetta, our software for protein design and structure prediction. The funding will also allow us to invest in the equipment, supplies and lab space needed to design and test millions of synthetic proteins. What challenges will we be tackling? Watch my [Link] TED talk to find out. All of this work — like everything we do — will depend on you, the participants in Rosetta@home. Whether it’s creating custom nanomaterials or safer cancer therapies, we rely on the Rosetta@home distributed computing platform. We cannot thank you enough for taking the time to be a part of this exciting research, and we hope you tell at least one friend that they too can play a role in the protein design revolution just by running Rosetta@home. Thank you, David Baker Director, Institute for Protein Design

By rosetta@home at 2019-07-16

Coevolution at the proteome scale

Last week, a report was published in [Link] Science describing the identification of hundreds of previously uncharacterized protein–protein interactions in E. coli and the pathogenic bacterium M. tuberculosis. These include both previously unknown protein complexes and previously uncharacterized components of known complexes. This research was led by postdoctoral fellow Qian Cong and included former Baker lab graduate student [Link] Sergey Ovchinnikov, now a John Harvard Distinguished Science Fellow at Harvard. Rosetta@home was used for much of the computing required for this work. Congratulations and thank you to all R@h volunteers. For more information about this work [Link] click here.

By rosetta@home at 2019-07-15

Protein arrays on mineral surfaces

Last week, the [Link] Baker Lab in collaboration with the [Link] De Yoreo lab at PNNL published a report in [Link] Nature describing the design of synthetic protein arrays that assemble on the surface of mica, a common and exceptionally smooth crystalline mineral. This work provides a foundation for understanding how protein-crystal interactions can be systematically programmed. Although R@h was not directly used for this research, previously designed subunits were validated using R@h. Congratulations to all R@h volunteers and thank you for your continued contributions. For more details [Link] click here.

By rosetta@home at 2019-07-15

Batch Status Update

I have archived the completed batch status tables to their own page - the link is at the top of the batch status page. This should help to clean up the main batch status page. I have also added a table for the final search over {2,5} (subfield 7). The immediate goal is still to complete sf4, followed by sf3, but I will be dropping in some small batches for sf7 periodically to help set the stage for the future search over sf7.

By numberfields@home at 2019-07-13

Science non-stop: another paper, another badge

...and here's another badge for another publication issued in 2018, [Link] Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs. This one is also on Sci. Rep., open access. Here, the authors used Gpugrid-based simulations to reconcile experimental results on Dopamine D3 receptor antagonists with their molecular structures. They used the large-scale high-throughput molecular dynamics with Markov state models (MSMs) to determine an alternative and possibly elusive pose ("cryptic") consistent with the mutation data. Thanks to every contributor! Noelia Ferruz, Stefan Doerr, Michelle A. Vanase-Frawley, Yaozhong Zou, Xiaomin Chen, Eric S. Marr, Robin T. Nelson, Bethany L. Kormos, Travis T. Wager, Xinjun Hou, Anabella Villalobos, Simone Sciabola & Gianni De Fabritiis Dopamine D3 receptor antagonist reveals a cryptic pocket in aminergic GPCRs Scientific Reportsvolume 8, Article number: 897 (2018) The recent increase in the number of X-ray crystal structures of G-protein coupled receptors (GPCRs) has been enabling for structure-based drug design (SBDD) efforts. These structures have revealed that GPCRs are highly dynamic macromolecules whose function is dependent on their intrinsic flexibility. Unfortunately, the use of static structures to understand ligand binding can potentially be misleading, especially in systems with an inherently high degree of conformational flexibility. Here, we show that docking a set of dopamine D3 receptor compounds into the exist...

By gpugrid at 2019-07-13

M Queens for arm64

We released now also a M Queens app for arm64.

By yoyo@home at 2019-07-11

More Nbody Runs on MilkyWay@home

Hey all, I've put up some more nbody runs for MilkyWay@home. Here are the names of the new runs: -de_nbody_07_10_2019_v176_40k__data__4 -de_nbody_07_10_2019_v176_40k__data__5 -de_nbody_07_10_2019_v176_40k__data__6 If you find any problems with these runs, please do not hesitate to contact us. Thank you all for your continued support! -Eric

By milkyway@home at 2019-07-10

New badge, new(ish) paper

Dears, we added a badge for a (not-so-recent-any-more) paper [Link] Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity. The abstract is here and the text is open-access. It is interesting because it provides evidence about the kinetics (i.e., transient conformational changes) incurred by the µ-opioid receptor (MOR) upon binding to drugs. MOR is part of the large and important GPCR protein family, which is targeted by approx ~30% of the current drugs. While the therapeutic effect of opioids analgesics is mainly attributed to µ-opioid receptor (MOR) activation leading to G protein signaling, their side effects have mostly been linked to β-arrestin signaling. To shed light on the dynamic and kinetic elements underlying MOR functional selectivity, we carried out close to half millisecond high-throughput molecular dynamics simulations of MOR bound to a classical opioid drug (morphine) or a potent G protein-biased agonist (TRV-130). Statistical analyses of Markov state models built using this large simulation dataset combined with information theory enabled, for the first time: a) Identification of four distinct metastable regions along the activation pathway, b) Kinetic evidence of a different dynamic behavior of the receptor bound to a classical or G protein-biased opioid agonist, c) Identification of kinetically distinct conformational states to be used for the rational design of functionally selective ligands that may eventually be developed into improved drugs; ...

By gpugrid at 2019-07-09

M Queens M=27 started

The 27x27 board is the highest-order board that has been completely enumerated. In 2016, after more than a year of computation on FPGA, 29,363,495,934,315,694 solutions were enumerated at University of Dresden. We want ot verify this number and have to run 2.2 million workunits, which we compute twice. On the progress bar you see 25% of it. We'll see if we need also a year for this.

By yoyo@home at 2019-07-08

New SETI Perspectives: "Seeing the Unseeable: The Black Hole Image"

Richard Lawn has posted another interesting article to "SETI Perspectives". This one is titled [Link] Seeing the Unseeable: The Black Hole Image and is about the Event Horizon Telescope's image of the black hole in M87.

By seti@home at 2019-07-05

Native ATLAS and Theory applications require a CVMFS configuration update

Volunteers running ATLAS native and/or Theory native are kindly asked to update their local CVMFS configuration. Please see the following [Link] post for the details.

By lhc@home_classic at 2019-07-05


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