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Rosetta@home

  • Coevolution at the proteome scale

    Posted: July 15, 2019, 9:23pm CEST


    Last week, a report was published in 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 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 click here.
  • Protein arrays on mineral surfaces

    Posted: July 15, 2019, 9:12pm CEST


    Last week, the Baker Lab in collaboration with the De Yoreo lab at PNNL published a report in 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 click here.

PrimeGrid

  • 50th Anniversary of the Moon Landing Challenge starts July 15th 20:17 UTC

    Posted: July 15, 2019, 12:42pm CEST
    "Thirty seconds and counting. Astronauts report it feels good. T-25 seconds. Twenty seconds and counting. T-15 seconds, guidance is internal. 12, 11, 10, 9 ... ignition sequence start ... 6, 5, 4, 3, 2, 1, 0 ... All engines running. Liftoff! We have a liftoff ... 32 minutes past the hour, liftoff on Apollo 11!" To celebrate the 50th Anniversary of humans landing on the Moon, PrimeGrid is running a 5 day challenge from July 15th 2019, 20:17 UTC until July 20th, 20:17 UTC. Work units from the PPS (LLR) project, which are downloaded and completed during the challenge will count towards your challenge score. Many primes are expected to be found. For more information and discussion, please see the official challenge thread: [www.primegrid.com]

GPUGRID

  • Science non-stop: another paper, another badge

    Posted: July 13, 2019, 10:36am CEST
    ...and here's another badge for another publication issued in 2018, 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 existing eticlopride-bound dopamine D3 receptor (D3R) X-ray crystal structure resulted in poses that were not consistent with results obtained from site-directed mutagenesis experiments. We overcame the limitations of static docking by using large-scale high-throughput molecular dynamics (MD) simulations and Markov state models (MSMs) to determine an alternative pose consistent with the mutation data. The new pose maintains critical interactions observed in the D3R/eticlopride X-ray crystal structure and suggests that a cryptic pocket forms due to the shift of a highly conserved residue, F6.52. Our study highlights the importance of GPCR dynamics to understand ligand binding and provides new opportunities for drug discovery.

yoyo@home

MilkyWay@home:

  • More Nbody Runs on MilkyWay@home

    Posted: July 10, 2019, 9:04pm CEST
    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

GPUGRID

  • New badge, new(ish) paper

    Posted: July 9, 2019, 12:08pm CEST
    Dears, we added a badge for a (not-so-recent-any-more) paper 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. Abhijeet Kapoor, Gerard Martinez-Rosell, Davide Provasi, Gianni de Fabritiis & Marta Filizola Dynamic and Kinetic Elements of µ-Opioid Receptor Functional Selectivity Scientific Reports volume 7, Article number: 11255 (2017)

    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; d) Characterization of multiple activation/deactivation pathways of MOR, and e) Suggestion from calculated transition timescales that MOR conformational changes are not the rate-limiting step in receptor activation.

yoyo@home

  • M Queens M=27 started

    Posted: July 9, 2019, 12:00am CEST
    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.

PrimeGrid

  • GFN-524288 Mega Prime!

    Posted: July 8, 2019, 2:20pm CEST
    On 29 June 2019, 00:54:18 UTC, PrimeGrid’s Generalized Fermat Prime Search found the Generalized Fermat mega prime: 2877652^524288+1 The prime is 3,386,397 digits long and enters Chris Caldwell's The Largest Known Primes Database ranked 3rd for Generalized Fermat primes and 26th overall. The discovery was made by Roman Vogt (Tabaluga) of Germany using an NVIDIA GeForce GTX 1060 in an Intel(R) Core(TM) i7-2700K CPU @ 3.50GHz CPU with 16GB RAM, running Windows 10. This GPU took about 1 hour and 42 minutes to probable prime (PRP) test with GeneferOCL5. Roman is a member of the Sicituradastra. team. The PRP was verified on 29 June 2019, 08:52:47 by Carlo Villa (carlo) using an NVIDIA GeForce 830M in an Intel(R) Core(TM) i5-5200U CPU @ 2.20GHz with 8GB RAM, running Windows 10. This GPU took about 16 hours and 55 minutes to probable prime (PRP) test with GeneferOCL5. The PRP was confirmed prime by an Intel(R) Xeon(R) CPU E3-1240 v6 @ 3.70GHz with 4GB RAM, running Linux. This computer took about 25 hours 53 minutes to complete the primality test using multithreaded LLR. For more details, please see the official announcement.

SETI@home: News

yoyo@home

  • M Queens for M=27

    Posted: July 5, 2019, 12:00am CEST
    With our last run for M=24 we verified the Windows app and the validation against Linux. With our test runs we were able to confirm the amount of solutions for M=21 and M=24. So now we are ready for M=27. Some workunits are already created.
  • Windows App for M Queens

    Posted: July 3, 2019, 12:00am CEST
    The Windows version of the M Queens app is now available together with some workunits for M=21 to test the windows version and the validation against the Linux version.
  • New Project M Queens

    Posted: June 30, 2019, 12:00am CEST
    We started M Queens as new project in yoyo@home.The M queens puzzle is the problem of placing M chess queens on an M x M chessboard so that no two queens threaten each other; thus, a solution requires that no two queens share the same row, column, or diagonal. Curently it is a test application only available for Linux64 and we are running some test workunits for M=24. We did already M=20 and verified the results. As next step we will verfy the number of solutions for M=27. If everything runs well we might go to find solutions for M=28, which is currently unknown.

PrimeGrid

  • Another New SR5 Mega Prime!

    Posted: June 28, 2019, 10:11pm CEST
    On 23 June 2019, 14:39:48 UTC, PrimeGrid’s Sierpiński/Riesel Base 5 Problem project eliminated k=322498 by finding the mega prime: 322498*5^2800819-1 The prime is 1,957,694 digits long and enters Chris Caldwell's “The Largest Known Primes Database” ranked 63rd overall and is the largest known base 5 prime. 67 k’s now remain in the Riesel Base 5 problem. The discovery was made by Jordan Romaidis of the United States using an Intel(R) Xeon(R) Gold 5120 CPU @ 2.20GHz with 96GB RAM running Microsoft Windows 10 Enterprise x64 Edition. This computer took 25 hours and 28 minutes to complete the primality test using multithreaded LLR. Jordan is a member of the San Francisco team. The prime was verified on 24 June 2019, 20:59:33 UTC by Scott Brown of the United States using an AMD FX(tm)-8350 Eight-Core Processor with 16GB RAM running Microsoft Windows 10 Core x64 Edition. This computer took about 53 hours and 51 minutes to complete the primality test using multithreaded LLR. Scott is a member of the Aggie The Pew team. For more details, please see the official announcement.
  • New SR5 Mega Prime!

    Posted: June 28, 2019, 9:55pm CEST
    On 21 June 2019, 01:30:42 UTC, PrimeGrid’s Sierpiński/Riesel Base 5 Problem project eliminated k=88444 by finding the mega prime: 88444*5^2799269-1 The prime is 1,956,611 digits long and enters Chris Caldwell's “The Largest Known Primes Database” ranked 63rd overall and is the largest known base 5 prime. 68 k’s now remain in the Riesel Base 5 problem. The discovery was made by Scott Brown of the United States using an Intel(R) Core(TM) i7-8700 CPU @ 3.20GHz with 32GB RAM running Microsoft Windows 10 Professional x64 Edition. This computer took 5 hours and 29 minutes to complete the primality test using multithreaded LLR. Scott is a member of the Aggie The Pew team. The prime was verified on 21 June 2019, 14:50:01 UTC by Dave Sunderland (DaveSun) using an Intel(R) Core(TM) i7-6700HQ CPU @ 2.60GHz with 16GB RAM running Microsoft Windows 10 Core x64 Edition. This computer took about 12 hours and 32 minutes to complete the primality test using multithreaded LLR. For more details, please see the official announcement.

SRBase: News

  • base S743 proven

    Posted: June 27, 2019, 6:42pm CEST
    On 15th of June, Doug, a member of the team Gridcoin found the last prime for base S743.
    The prime 10*743^285478+1 has 819606 digits and entered the TOP5000 in Chris Caldwell's The Largest Known Primes Database.
  • base S780 proven

    Posted: June 26, 2019, 5:18pm CEST
    On 02th of June, CharityEngine2, a member of the team Gridcoin found the last prime for base S780.
    The prime 43*780^205685+1 has 594863 digits and entered the TOP5000 in Chris Caldwell's The Largest Known Primes Database.

BOINC

  • BOINC@TACC article

    Posted: June 26, 2019, 7:13am CEST
    Check out For the Love of Science, a new article about the BOINC@TACC project at the Texas Advanced Computing Center.
  • BOINC web server failure

    Posted: June 26, 2019, 5:09am CEST
    The machine hosting the BOINC web site, and Science United, failed last Friday, just after everyone had left for the weekend. Fortunately we were able to move the disks to another computer and we're back online as of this morning. We apologize for the inconvenience.

Universe@Home: News

  • Server upgrade

    Posted: June 24, 2019, 10:39pm CEST
    For next few days I will not generate more tasks as I'm preparing to server software update.
    The software will require few restarts and is planned later in this week - I will inform you when it happens exactly.