News from BOINC Projects

Recent items from the news feeds of various BOINC projects.

[SRBase] Trial Factoring 75-76bit range started

The next batch of 50k tests is uploading.

The runtime is now ~2h40min on a RX5500 XT and decreasing on higher ranges.

View article · Thu, 11 Jul 2024 10:02:09 +0000


[SIDock@home] Target # 23: Ebola GP1

Dear participants,

as target # 22 is almost finished, we are glad to introduce the next target. Most of you have voted for Ebolavirus glycoprotein (GP) (174 out of 425 votes, wow!)

The Ebola virus is a highly virulent pathogen responsible for causing Ebola hemorrhagic fever, a severe and often fatal disease. A key factor in the virus's ability to infect host cells and cause disease is its surface glycoprotein (GP), making it an attractive target for antiviral drug development. The Ebola GP is a trimeric protein composed of two subunits per monomer: GP1, responsible for receptor binding, and GP2, which mediates fusion between the viral and host cell membranes. Initially synthesized as a precursor protein, the GP is cleaved by host proteases (furin, cathepsin) into its functional subunits, a process essential for its role in mediating viral entry. The GP facilitates the virus's attachment to the host cell surface, followed by conformational changes that enable membrane fusion, allowing the virus to enter the host cell (to the host endosomal Niemann-Pick C1 (NPC1) receptor or via direct membrane binding; Vaknin et al.; ACS Infect. Dis. 2024, 10, 5, 1590–1601).

Targeting the GP for drug development is advantageous due to its essential role in viral infection, its highly conserved structure among different Ebola virus strains, and the availability of specific binding cavities that can accommodate small-molecule inhibitors. Structural studies using techniques such as X-ray crystallography have identified these binding cavities and elucidated the GP's conformation in both its free and inhibited states. These insights enable the design of drugs that can specifically bind to and inhibit the GP by stabilizing it in its pre-fusion conformation or interfering with its cleavage, thereby preventing the necessary conformational changes for membrane fusion. We will employ high-resolution structures to conduct virtual screening experiments coupled to molecular dynamics simulations to ultimately identify potential GP inhibitors/modulators.

Promising compounds identified through these computational methods will hopefully undergo further validation using biochemical assays, pseudovirus entry assays, and structural analyses to confirm their inhibitory activity. Targeting the GP offers specificity, as it minimizes off-target effects on host cells and reduces the likelihood of resistance development. Moreover, due to the conserved nature of the GP, drugs targeting it could be effective against multiple Ebola virus strains and variants.

We hope that our computations will contribute to the fight against Ebola!

View article · Thu, 11 Jul 2024 09:02:55 +0000


[World Community Grid] Research Update from the MCM team (July 2024)

We continue to characterise lung cancer biomarkers identified in the MCM1 project. This update focuses on ASTN2, a protein involved in neuronal migration. It is expressed across several tissue types, and has been implicated in various cancers.

View article · Wed, 10 Jul 2024 21:25:48 +0000


[PrimeGrid] Project finances

Please visit the forums to find an update on the project finances. Any donations for the project are greatly appreciated. Please visit the donations page if you want to support the project financially. Thank you!

View article · Tue, 18 Jun 2024 10:56:33 +0000


[YAFU] Aliquot sequence 2896896 has terminated!!!

Aliquot sequence 2896896 has terminated!!!

View article · Mon, 17 Jun 2024 17:31:55 +0000


[Climateprediction.net] New batch going out to volunteer's machines: STORMS, investigating how low-pressure systems may change in the future

Project: Quantifying controls on the intensity, variability and impacts of extreme European STORMS
by Clément Bouvier and Victoria Sinclair (University of Helsinki)

Throughout the year, low-pressure systems regularly move across Europe, usually from west to east, bringing cloud, rain and windy weather. Sometimes these weather systems can become very intense, and the winds and rain associated with them can cause damage to buildings and infrastructure, flooding, and can disrupt electricity supply and travel. Although the short-term weather forecasts of these storms are now quite accurate, it still remains uncertain how these storms, and their impacts, are likely to change in the future as our climate changes. Some of this uncertainty is because our understanding of what controls the strength and impacts of these storms is incomplete.

The aim of this project is to understand what controls the strength and structure of these low-pressure systems. We will quantify how the atmospheric state that the low-pressure systems develop in affects the strength and structure of these low-pressure systems. This atmospheric state can be described by various parameters, for example, the mean temperature, moisture content, and upper-level wind speeds (i.e. the strength and width of the jet stream). Since there are lots of different parameters we want to study (not just the ones described above), we want to do lots of experiments in a high controlled manner. Therefore, we will run a large ensemble of simulations of idealised low-pressure systems using the numerical weather prediction model OpenIFS. Although the simulations are idealised, the weather systems that develop look very like real weather systems that we observed in reality. Each ensemble member differs in its initial atmospheric state, and we choose these initial states to cover everything from the current climate to past pre-industrial climates to the most extreme future climate projections. This is exciting because although idealised simulations of low-pressure systems have been performed before, this is the first time that such an extensive exploration of the parameter space will be conducted.

Once we have the results from the large ensemble, we will calculate different measures of the strength of the storms and then use machine learning techniques to see how these relate to the initial states. Our results will hopefully increase in confidence in how these storms and their impacts will change in the future.

Technical information:
Run time: between 8 and 9 hours for 1 workunit (1 core, Xeon Gold 6230)
Number of files: 480 files
Maximum size of individual files: 1.3MB for 2D fields output files, 13.3MB for spectral output files, 7.1MB for 3D fields output files
Total disk load: 2.0GB

View article · Wed, 12 Jun 2024 19:58:43 +0000


[SRBase] The server / project is restarted now

There is a slow progress from rehab but not happy with the results yet. All of the recovering is very slowly with restrictions.

The RAM was tested in the first run and looking ok.

I will test some work too.

I really missed the last pentathlon. Hoping to finish the TF range of GIMPS work too.

View article · Tue, 11 Jun 2024 15:27:16 +0000


[PrimeGrid] PrimeGrid's 19th Birthday Challenge

From June 12th 19:00:00 UTC to June 19th 19:00:00 PrimeGrid will be running a 7 day challenge on the GFN-19 project. The start and end times are comparatively usual. For more information, please see this forum thread.

View article · Sun, 9 Jun 2024 05:55:41 +0000


[ODLK1] Electrical work 3

I just being informed now that tomorrow 29/05/2024 in my area there will be another electrical power off from 9:00 to 16:00!!!!

This means that battery power supply cannot handle 7 hours of power failure, so I need to program that the server shot down automatically before 9:00 to preserve it.

It need to be manually power on and this could be done at 19:00.

Sorry for the problems.

Thanks

View article · Tue, 28 May 2024 16:47:48 +0000


[NFS@home] BOINC Pentathlon - Thank you!

Thank you to all the BOINC Pentathlon participants who devoted their time and computing power to NFS@Home, and to SETI.Germany for organizing this event. We look forward to next time!

View article · Tue, 21 May 2024 01:00:21 +0000


[ODLK] The ODLK project is 7 years old!

С Днём Рождения!

Happy birthday!

View article · Sun, 19 May 2024 01:53:54 +0000


[YAFU] Aliquot sequence 2912730 has terminated!!!

Aliquot sequence 2912730 has terminated!!!

View article · Sat, 18 May 2024 12:22:20 +0000


[RakeSearch] Processing of the square # 38 completed

Dear participants, processing of the square # 38 is fully completed! The square:

0 1 2 3 4 5 6 7 8 9 A B
1 2 3 B 5 7 4 9 0 A 6 8
9 A 6 4 8 0 B 1 7 2 3 5
A 6 4 5 0 1 8 2 9 3 B 7
7 9 A 6 B 8 3 0 5 1 2 4
2 3 B 8 7 9 5 A 1 6 4 0
8 0 1 2 6 4 A 5 B 7 9 3
6 4 5 7 1 2 0 3 A B 8 9
5 7 9 A 3 B 2 8 4 0 1 6
4 5 7 9 2 3 1 B 6 8 0 A
B 8 0 1 A 6 9 4 3 5 7 2
3 B 8 0 9 A 7 6 2 4 5 1

has 541571814 orthogonal mates which puts it on the 26th place of the rating which include now 5711 positions.

Now "high part" of spectra of ODLS-12 looks like this (square # 38 marked by red):


Thank you for project attention, support and donation of CPU time!

View article · Fri, 17 May 2024 19:35:50 +0000


[RakeSearch] Processing of the square # 37 completed

Dear participants, processing of the square # 37 is fully completed! The square:

0 1 2 3 4 5 6 7 8 9 A B
1 2 0 4 5 3 8 B 9 6 7 A
6 8 9 A 7 B 1 5 2 0 4 3
5 3 4 1 2 0 B 9 A 7 8 6
9 6 8 B A 7 0 4 1 2 3 5
B A 7 8 9 6 3 0 4 5 2 1
A 7 B 9 6 8 4 1 5 3 0 2
4 5 3 0 1 2 7 8 B A 6 9
7 B A 6 8 9 5 2 3 4 1 0
3 4 5 2 0 1 A 6 7 B 9 8
8 9 6 7 B A 2 3 0 1 5 4
2 0 1 5 3 4 9 A 6 8 B 7

has 527873490 orthogonal mates which puts it on the 28th place of the rating which include now 5684 positions.

Now "high part" of spectra of ODLS-12 looks like this (square # 37 marked by red):


Thank you for project attention, support and donation of CPU time!

View article · Fri, 17 May 2024 19:33:31 +0000


[ODLK1] Electrical work 2

It seems that in my area electrical works are every month!

On 16/05/2024 from 9:00 to 13:00 there is no electrical power in the area again, so no connection to server (power supply should be able to carry the 4h of power off and still run the server, but without connection to internet).

Thanks

View article · Mon, 13 May 2024 17:17:53 +0000


[World Community Grid] Research update from the MCM team (May 2024)

We continue to characterise lung cancer biomarkers identified in the MCM1 project. This update focuses on KLF5, a well-studied gene that has been implicated in several cancer types. KLF5 is a transcription factor, which is expressed across numerous organs and tissues.

View article · Mon, 13 May 2024 15:27:39 +0000


[NFS@home] BOINC Pentathlon

Welcome BOINC Pentathlon participants. NFS@Home has been chosen for the Javelin Throw discipline starting May 10 at midnight UTC.

View article · Thu, 9 May 2024 16:31:16 +0000


[ODLK1] Some issues

I just see today that the OS update of some days ago has stopped something in connection.

Now I reboot all to be sure new kernel were loaded.

Actually log seems good, so I hope that the Boinc activity is restored good.

Thanks

View article · Tue, 7 May 2024 19:15:16 +0000


[YAFU] Aliquot sequence 2776776 has terminated!!!

View article · Tue, 7 May 2024 18:30:22 +0000


[SRBase] server shutdown on 20.05.

In absence and rehab the project will be shutdown for a month to recover.

A full restart is planned after that if nothing else occured.

If you want to contact me in this time Iam still reached in discord forums.

Many thanks for understanding!

View article · Tue, 7 May 2024 17:51:13 +0000


[YAFU] Aliquot sequence 2956992 has terminated!!!

Aliquot sequence 2956992 has terminated!!!

View article · Sat, 4 May 2024 07:49:25 +0000


[GPUGrid.net] In-silico Binding Assay (ISBA/ACEMD3)

This is a message Adrià posted in our discord channel. Since he doesn't have an account in the GPUGRID forum I open the thread for him. If you want to be more up to date to the news related to this project and others please join our discord, we are usually more active there: https://discord.gg/dCMkcafPpX

Hello GPUGRID! Here Adrià. I'll be recovering the ACEMD3 application again, and sending new jobs of standard MD simulations (We've been testing it these past weeks to make sure it worked well for both Windows and Linux) The main goal of these new batch of simulations will be to validate further our capacity to predict the binding mode of ligands using simulations and adaptive sampling methods. Those of you that have been around for some time here might already be familiar with these simulations, such as the Benzamidin-Trypsin system (https://www.pnas.org/doi/abs/10.1073/pnas.1103547108) or the Dopamine D3 receptor with an antagonist ligand (https://www.nature.com/articles/s41598-018-19345-7#Ack1), which we were able to simulate thanks to GPUGRID and all your effort! Now, we are revisiting this method, which we call in-silico binding assay (ISBA). During drug discovery campaings, it's common that you know of ligands that bind to your target, but you don't know their binding mode, the exact conformation and structure that both the ligand and the protein have when bound. Knowing the binding mode is critical for further development of the molecule into a potent and usable drug. The most precise way of discovering the binding mode is with crystallization. However, that can take too much time or be directly impossible, depending on the protein. Therefore, we want to optimize and refine ISBA for binding mode prediction, so it can be usable during drug discovery projects. To summarize a bit our objectives, we want to predict binding modes for larger molecules than Benzamidin, with the same precision, but with less simulation time that was needed for the D3 receptor system. To do so, we'll be using the latest version of adaptive sampling that we developed, AdaptiveBandit (https://pubs.acs.org/doi/abs/10.1021/acs.jctc.0c00205). The objective of these new simulations I'll be sending will be to benchmark AdaptiveBandit in an ISBA scenario, improve the algorithm if required and fine-tune its hyperparameters. Let me know if there's any issue with the simulations. I'll be sending 100ns trajectories for the most part, divided in two steps.

View article · Thu, 2 May 2024 09:28:34 +0000




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