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Enhancing ECM range
I'm enhancing the ecm search range for B1=43e6 up to 2000 digits. Some test workunits are already send out with the name ecm_es_*test* and a short deadline of 1 day. Together with this the credit formula was changed.
New Runs for MilkyWay@home Nbody Simulations (07/29/2020)
I just wanted to let everyone know that new Nbody runs have been put up on MW@home. The last set of runs started converging nicely, so we are confident this next set of runs will converge as well. The names of these runs are:
Please let us know if you have any trouble with these runs. Thank you all for your continued support.
Scheduled Internet Outage July 28th,2020
On July 28th, our server will be temporarily inaccessible due to a scheduled campus-wide internet outage. As such, job queues may not update for the day. However, everything should return to working order by the next day. We apologize for any inconvenience this may cause.
New paper 2/2: GPCRmd uncovers the dynamics of the 3D-GPCRome
The second paper is
Rodríguez-Espigares, I., Torrens-Fontanals, M., Tiemann, J.K.S. et al. GPCRmd uncovers the dynamics of the 3D-GPCRome. Nat Methods (2020). [Link] 10.1038/s41592-020-0884-y
here, your computations have been used to build a database of configurations for most types and subtypes of GPCR-class proteins. GPCRs are "do-all" receptors - there are many many subtypes, each with activators and inhibitors. The [Link] GPCRmd database provides for the first time a *systematic* coverage of their dynamics.
G-protein-coupled receptors (GPCRs) are involved in numerous physiological processes and are the most frequent targets of approved drugs. The explosion in the number of new three-dimensional (3D) molecular structures of GPCRs (3D-GPCRome) over the last decade has greatly advanced the mechanistic understanding and drug design opportunities for this protein family. Molecular dynamics (MD) simulations have become a widely established technique for exploring the conformational landscape of proteins at an atomic level. However, the analysis and visualization of MD simulations require efficient storage resources and specialized software. Here we present GPCRmd (http://gpcrmd.org/), an online platform that incorporates web-based visualization capabilities as well as a comprehensive and user-friendly analysis toolbox that allows scientists from different disciplines to visualize, analyze and share GPCR MD data. GPCRmd originates from a com...
New paper 1/2: PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulation
Two recent papers which came out with results from GPUGRID.
PlayMolecule CrypticScout: Predicting Protein Cryptic Sites Using Mixed-Solvent Molecular Simulations
Gerard Martinez-Rosell, Silvia Lovera, Zara A. Sands, and Gianni De Fabritiis
Journal of Chemical Information and Modeling 2020 60 (4), 2314-2324
In this paper (and the corresponding live system) GPUGRID's computations are used to power a search for elusive (transient) pockets which may become drug targets.
Thanks for the contributions!
Cryptic pockets are protein cavities that remain hidden in resolved apo structures and generally require the presence of a co-crystallized ligand to become visible. Finding new cryptic pockets is crucial for structure-based drug discovery to identify new ways of modulating protein activity and thus expand the druggable space. We present here a new method and associated web application leveraging mixed-solvent molecular dynamics (MD) simulations using benzene as a hydrophobic probe to detect cryptic pockets. Our all-atom MD-based workflow was systematically tested on 18 different systems and 5 additional kinases and represents the largest validation study of this kind. CrypticScout identifies benzene probe binding hotspots on a protein surface by mapping probe occupancy, residence time, and the benzene occupancy reweighed by the residence time. The method is presented to the scientific community in a web application available via www.playmolecule.org using a distributed computing infrastructure to perform the simulations.
List of mo...
Server outage resolved
I am sorry for server outages which was happening recently. There were several factors which often caused lack of free space and some services crashed and I had to do an emergency shutdown on Saturday in order to fix everything so I couldn't inform you about it except for Twitter. There is still a hardware problem with one of servers which I have to fix but the server is not being used now so project should be stable now.
Radim Vančo (FoxKyong)
New Runs for MilkyWay@home Nbody Simulations (07/07/2020)
The last set of N-body runs we set up started converging to compact progenitors due to an overly restrictive data histogram. We have fixed the data histogram and placed new runs up on the server:
Please let us know if these runs cause any problems, and thank you all for your support.
CMS job rundown
We need to do some tests of a patch to fix a bug that's been plaguing us for some time. To this end, I am letting the job queues drain, so there will be an absence of CMS jobs -- perhaps as soon as tomorrow morning, depending on how we continue to recover from today's Oracle quota problem.
So, be prepared to set No New Tasks as soon as you see any sign of lack of jobs -- or sooner if you prefer.
I don't know how long the testing will take, there are many factors at work (if the BOINC server sees that there are no jobs available, it will stop sending tasks; that will mean it takes longer for each test batch to be recognised and start serving jobs).