Changes in task scheduling and monitoring mechanism
Dear participants, at the start of current search we set deadline for "CMDock long tasks" to 14 days or 336 hours. But average time required to process an individual task is 40 hours. Also, we see, that many of uncompleted tasks which prevent completion of the set to which they belong, "produced" by computers that catch some tasks and didn't get in touch again. Due this, we plan:
1. To perform a gradual reduction of the deadline;
2. To implement a simple mechanism which finds computers that are lost in computing space (those who did not send requests to the server in last m days), and mark its tasks as lost. For example, m may be 10, 8, 6 or 5.

This should not interfere with computers actually participating in the calculations, but can be greatly enhance "results logistic".
6 Nov 2023, 10:05:37 UTC · Discuss

BOINC merchandise by the Science Commons Initiative
Dear participants,

There is a wonderful new beginning started by the Science Commons Initiative. They launched a web store selling BOINC-related merchandise. SiDock@home is already on board :)

We support this idea and hope it will help more people to know about BOINC and get interested in BOINC projects! It will also contribute to the development of BOINC as 50% of the profits will go to the BOINC Development Fund (100% in special cases). Another 50% of the profit will go to the project as a donation.

With best wishes,
team of SiDock@home
23 Feb 2023, 9:29:38 UTC · Discuss

Target # 22: corona_RdRp_v2
Dear participants,

After doing initial studies on an established SARS-CoV-2 target RNA dependent RNA polymerase (RdRp), we are departing from protease studies and focus on RdRp along with additional NSP targets. Namely, RdRp (NSP12), is responsible for the transcription of viral genes and ultimately replication of the viral genome. The studied active site binds RNA and was previously studied in the context of remdesivir, galidesivir, molnupiravir and several other small molecules. Further reading below:

• Structure of replicating SARS-CoV-2 polymerase
  
• Identification of novel SARS-CoV-2 RNA dependent RNA polymerase (RdRp) inhibitors: From in silico screening to experimentally validated inhibitory activity
  
• RNA dependent RNA polymerase (RdRp) as a drug target for SARS-CoV2
  
• Ribavirin, Remdesivir, Sofosbuvir, Galidesivir, and Tenofovir against SARS-CoV-2 RNA dependent RNA polymerase (RdRp): A molecular docking study
  

Figure 1: RdRp in white color along with RNA chain and N4-hydroxycytidine from Molnupiravir in the active site (red stick model).

With best wishes,
Natalia, Marko, Črtomir, hoarfrost.
15 Jan 2023, 17:45:23 UTC · Discuss

СmDock "long" and "short" tasks applications
Dear participants!

We created new applications named as "CurieMarieDock 0.2.0 long tasks" and "CurieMarieDock 0.2.0 short tasks", both based on CmDock 0.2.0 release. Algorithm of both applications are identical, but for "short tasks" we created only ARM-version and we plan to generate a special, smaller in 5 times tasks that covers one of part of entire tasks set. We advice all owners of small single-board computers like Raspberry Pi, to switch to "short tasks" application.

In next 1 .. 2 days we continue to generate new tasks "Sprot_delta_v1" (extended run) for both application, but later we issue a sample tasks set for new target (# 22) and only for "long application" because all task of sample set will be large. Simultaneously, project will continue to send Sprot_delta_v1 tasks for "short" application. And then we will proceed to sent long and short tasks for appropriate applications.

Hope that this explanation makes situation is clear.

Thank you for participation and donation of CPU time!
13 Jan 2023, 23:35:04 UTC · Discuss

Merry Christmas!
Dear participants,

We wish you a merry Christmas and a happy New Year!

With your help, we have performed a lot of computer modeling. We are going to continue, and believe the results will lead to advances in drug development! For now, we have a fresh new release of CmDock and will employ it starting from the next target. Here is an illustration of the modeling performed in the project, visualized with PyMOL. You can see a large molecule (this is the target, TMPRSS2 protein) with a molecule many times smaller. The small molecules are ligands, each of them can interact with the target in its own way, with its own binding energy.

The more precisely the ligand binds to the target, the higher the chance that it will be able to change the functioning of the large molecule. For example, the TMPRSS2 enzyme shown in the image is necessary for a chemical reaction allowing the coronavirus to enter the body cells and, accordingly, a substance that can suppress the normal operation of this enzyme can make it difficult or block the spread of the coronavirus in it. During the modeling performed on your computers, various ligands from the library are tested, and the best ones are selected to process on next stages of drug development.

All the best,
Natalia, Marko, hoarfrost, Črtomir


24 Dec 2022, 17:13:03 UTC · Discuss

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Sidock@home is an international volunteer computing project aimed at drug discovery. The first mission of the project is discovery of possible drugs against the SARS-CoV-2 virus. It started as an extension of the project  COVID.SI to engage the BOINC community into the drug discovery.

You can help with your computer. With the help of BOINC, you will download a subset of compounds on your computer, examine the compounds in the context of the studied target and send the results to a server where they are collected for later analysis.

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