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Právě je úterý, 22.září 2020, 12:49 hod.
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PrimeGrid 2020-09-21 20:19:56
321 Sieve is being SUSPENDED Nové okno
On October 21st, we will be suspending our 321 Sieve project. Details and discussion can be found here.

 
RNA World (beta) 2020-09-21 13:18:44
Small popular science article published in Laborjournal (German) Nové okno
Today, a brief popular science article dealing with the Rechenkraft.net community and the RNA World Projekt has appeared in the online version of the popular German lab journal 'Laborjournal' - unfortunately, this article is available only in German. Rechenkraft.net has spread the news already via Twitter.

Heute ist im Laborjournal (Online-Variante) ein kleiner deutschsprachiger Artikel zur Rechenkraft.net Community und unserem RNA World Projekt herausgekommen. Rechenkraft.net hat ihn auch schon über Twitter verbreitet.

Michael.

 
WEP-M+2 2020-09-19 12:52:09
12-digit factor of P2203 has now been found by the project... Nové okno
...259857 times

 
TN-Grid 2020-09-17 00:53:39
AMD COVID-19 HPC Fund Adds New Research Institutions Nové okno
Our gene@home project (hosted by the University of Trento, Italy) has been chosen by AMD as a recipient for their COVID-19 HPC fund, see the official announcement https://www.amd.com/en/corporate/hpc-fund

We are really grateful to receive this donation, it will give us access to high performance computing nodes, boosting our research. More info and comments here: https://gene.disi.unitn.it/test/forum_thread.php?id=291

 
Einstein 2020-09-10 07:39:27
Tenth anniversary of the first Einstein@Home discovery Nové okno

Ten years ago, Einstein@Home published its first astronomical discovery. The radio pulsar J2007+2722 was found in July 2010 with our radio pulsar search, analyzing data from the Arecibo Radio Telescope. The discovery appeared in print on 10 September 2010. A more detailed article about the discovery was published later.

read more


 
GPUGRID/PS3GRID 2020-09-09 11:24:39
New paper: Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations. Nové okno
Another great GPUGRID-based work: studying the possible modulation of intrinsically disordered proteins through drugs. Herrera-Nieto P, Pérez A, De Fabritiis G, Small Molecule Modulation of Intrinsically Disordered Proteins Using Molecular Dynamics Simulations. Journal of chemical information and modeling 2020. doi:10.1021/acs.jcim.0c00381 The corresponding badge is labeled "Herrera-Nieto, JCIM 2020".
The extreme dynamic behavior of intrinsically disordered proteins hinders the development of drug-like compounds capable of modulating them. There are several examples of small molecules that specifically interact with disordered peptides. However, their mechanisms of action are still not well understood. Here, we use extensive molecular dynamics simulations combined with adaptive sampling algorithms to perform free ligand binding studies in the context of intrinsically disordered proteins. We tested this approach in the system composed by the D2 sub-domain of the disordered protein p27 and the small molecule SJ403. The results show several protein–ligand bound states characterized by the establishment of a loosely oriented interaction mediated by a limited number of contacts between the ligand and critical residues of p27. Finally, protein conformations in the bound state are likely to be explored by the isolated protein too, therefore supporting a model where the addition of the small molecule restricts the available conformational space.

 
TN-Grid 2020-09-08 10:44:17
Server unreachable (2020-09-09, from 05:30 to 08:00 CEST) Nové okno
Wednesday 09/09, from 05:30 to 08:00 CEST, the IT services of UniTrento will not be available because of a planned IT maintenance. The TN-Grid server (hosted by UniTrento) will probably be not reachable during this period.

 
ATLAS 2020-09-07 08:22:24
BOINC database downtime Nové okno
The LHC@home database will be down for a while this morning, due to a network interruption in the CERN data centre. Hence scheduler requests and uploads will fail for a while.

Sorry for the trouble and happy crunching.

 
LHC 2020-09-07 08:22:24
BOINC database downtime Nové okno
The LHC@home database will be down for a while this morning, due to a network interruption in the CERN data centre. Hence scheduler requests and uploads will fail for a while.

Sorry for the trouble and happy crunching.

 
WEP-M+2 2020-09-06 09:34:45
Project backups Nové okno
Daily backups of the project no longer guaranteed

 
WEP-M+2 2020-09-06 09:32:56
Account creation suspended... Nové okno
...might be reopened for about 24 hours on the 19th

 
NFS 2020-09-03 22:38:37
Two new apps launched Nové okno
Two new apps have been launched, lasievee_small and lasievef_small. As the numbers we factor become larger, the lasieved app has largely become inadequate while the lasievee app queue has grown very long. In an attempt to compensate, job memory use and runtime has crept upward to stretch the capability of the apps. To alleviate these issues, these new apps will provide additional flexibility to choose the app most appropriate to the size of the number being factored while keeping memory use and runtime more reasonable. If you have modified your project preferences to run only specific applications, you may want to adjust your settings to enable these new apps. Thanks for your contributions to NFS@Home!

 
RakeSearch 2020-09-03 20:50:35
SAT-CMS-based search badge! Nové okno
Dear participants!

Most workunits of the SAT-CMS-based search of orthogonal diagonal Latin squares (ODLS) of order 10 has been completed, so we grant a new badge to participants whose computers found solutions in it. Each solution contains at least one pair of ODLS. Since Dr. Oleg Zaikin, the leading scientist of this study, works in Irkutsk, Siberia, he chose a wonderful Siberian animal Cabarga (or Siberian musk deer) to be depicted in the badge. After post-processing of results we are planning to publish full results of this search. However, the badge is given right now, and we send our warm congratulations to:

[AF>Libristes] Davlabedave (L'Alliance Francophone) and KySU,
Megacruncher TSBT (The Scottish Boinc Team) and applish,
scole of TSBT (The Scottish Boinc Team) and Rene Schimmer,
Cruncher Pete (The Scottish Boinc Team) and Bok (SETI.USA),
davidBAM (The Scottish Boinc Team) and yiqiL (Team China),
Konstantin Desyatkin (Russia Team) and Ufol (BOINC@Poland),
Rhodan71 (L'Alliance Francophone) and MaZZaY (Russia Team),
Ron Shurtz [BlackOps] (SETI.USA) and Odd-Rod (BOINCstats),
EarlyBird@Zircons (BOINC@Taiwan) and alexey (Russia Team),
KAMCOBILL (X Grubbers Kick Ass) and RFGuy_KCCO ([H]ardOCP),
=Lupus= (BOINC Confederation) and JagDoc (Planet 3DNow!),
boceli (Czech National Team) and CFJH (Rechenkraft.net),
DoctorNow (BOINC@Heidelberg) and Spritex (BOINC@Denmark),
Fardringle (TeAm AnandTech) and ssjy806 (SETIKAH@KOREA),
[B@P] Daniel (BOINC@Poland) and Woodles (UK BOINC Team),
ReaDy (Astronomy.Ru Forum) and zombie67 [MM] (SETI.USA),
Lycidas (BOINC@Heidelberg) and CoolAtchOk (Russia Team),
Sengieffe (UK BOINC Team) and Diffident (Overclock.net).

Only 36 participants received this badge!
Thank you for your attention to the project and donation of CPU time!

 
Einstein 2020-09-03 12:06:51
2020 BOINC Workshop - Call for Volunteers Nové okno

In light of the cancelation of the 2020 BOINC Workshop in Marburg, Germany, there will be a virtual celebration of BOINC projects, development, and community. As with all things BOINC, your help -- the BOINC community -- is needed to produce the event. Learn more below and at http://www.boincworkshop.org/.


 
GPUGRID/PS3GRID 2020-09-02 10:05:21
New paper: Computational and experimental characterization of NF023, a candidate anticancer compound inhibiting… Nové okno
Here we studied a possible mode of action of NF023, a molecule which disrupts some protein-protein interactions (cIAP-TRAF) misregulated in cancer. The molecule is very charged and flexible, so classical docking studies aren't up to a full modeling... but large-scale MD powered by GPUGRID is. Cossu F, Sorrentino L, Fagnani E, Zaffaroni M, Milani M, Giorgino T, Mastrangelo E. Computational and experimental characterization of NF023, a candidate anticancer compound inhibiting cIAP2/TRAF2 assembly. J Chem Inf Model. 2020 Aug 21 doi:10.1021/acs.jcim.0c00518
Protein-protein interactions are the basis of many important physiological processes, and are currently promising, yet difficult, targets for drug discovery. In this context, inhibitors of apoptosis (IAPs)-mediated interactions are pivotal for cancer cell survival; the interaction of the BIR1 domain of cIAP2 with TRAF2 was shown to lead the recruitment of cIAPs to the TNF-receptor, promoting the activation of NF-κB survival pathway. In this work, using a combined in silico-in vitro approach we identified a drug-like molecule, NF023, able to disrupt cIAP2 interaction with TRAF2. We demonstrated in vitro its ability to interfere with the assembly of the cIAP2-BIR1/TRAF2 complex and performed a thorough characterization of the compound’s mode of action through 248 parallel unbiased molecular dynamics simulations of 300 ns (totaling almost 75 µs of all-atom sampling), which identified multiple binding modes to the BIR1 domain of cIAP2 via clustering and ensemble docking. NF023 is, thus, a promising protein-protein interaction disruptor, representing a starting point to develop modulators of NF-κB-mediated cell survival in cancer. This study represents a model-procedure that shows the use of large-scale molecular dynamics methods to typify promiscuous interactors.

 
GPUGRID/PS3GRID 2020-08-31 11:17:38
Science pages updated Nové okno
Should now reflect the list of papers and badges. Some data, e.g. images, is missing.

 
CSG 2020-08-29 22:55:30
[all] status update Nové okno
It seems like it's back but who really knows without a posting by an Admin

 
GPUGRID/PS3GRID 2020-08-26 13:11:54
New paper: Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations Nové okno
The latest scientific publication obtained with your support and computation is here: Herrera-Nieto, P., Pérez, A. & De Fabritiis, G. Characterization of partially ordered states in the intrinsically disordered N-terminal domain of p53 using millisecond molecular dynamics simulations. Sci Rep 10, 12402 (2020). It investigates an open and difficult problem in biology, namely the structure-function relationship of intrinsically disordered proteins (IDP). IDP proteins are involved in many regulatory processes, and yet are difficult to study both experimentally and computationally. The amount of power provided by GPUGRID volunteers came to the rescue, enabling very extensive sampling of p53, an exemplary IDP involved in oncogenic processes.
The exploration of intrinsically disordered proteins in isolation is a crucial step to understand their complex dynamical behavior. In particular, the emergence of partially ordered states has not been explored in depth. The experimental characterization of such partially ordered states remains elusive due to their transient nature. Molecular dynamics mitigates this limitation thanks to its capability to explore biologically relevant timescales while retaining atomistic resolution. Here, millisecond unbiased molecular dynamics simulations were performed in the exemplar N-terminal region of p53. In combination with state-of-the-art Markov state models, simulations revealed the existence of several partially ordered states accounting for ∼ 40% of the equilibrium population. Some of the most relevant states feature helical conformations similar to the bound structure of p53 to Mdm2, as well as novel

 
WEP-M+2 2020-08-19 12:52:09
12-digit factor of P2203 has now been found by the project... Nové okno
...255580 times

 
MilkyWay 2020-08-17 18:35:48
Continued NBody Runs (07/29/2020) Nové okno
Hey everyone,

The last set of NBody runs have just converged beautifully. We are currently working on writing the paper to publish these results. In the meantime, we will be replacing these runs with another set:
-de_nbody_07_29_2020_v176_40k__data__4
-de_nbody_07_29_2020_v176_40k__data__5
-de_nbody_07_29_2020_v176_40k__data__6

Thank you all so much for your support. We would not be able to write this paper without your continued assistance.

-Eric


 Další

Thanks to David Vignoni for graphics and inspiration.


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