Target # 22: corona_RdRp_v2
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:
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
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
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
Release CmDock v 0.2.0
Dear SiDock@home community,
CmDock 0.2.0 is released:
-Cross-platform consistent random number generator (custom implementation of probability density functions); new switch -x defined, which turns on this feature.
-CI pipeline with regression testing
-logging in cmcavity
-cmcavity implementaiton of cavity volumes in InsightII (-I) or MRC 2014 (-M)
-Full protein surface mapping
-Pymol GUI plugin for Your demo/teaching/visualisation/research projects ;)
You can get it at:
Happy holidays to all!
, and all health!
Marko & CmDock team & SiDock@home team
14 Dec 2022, 16:02:58 UTC · Discuss
BOINC Census 2022, be counted!
The BOINC Census is a yearly effort aimed at finding out who uses BOINC, what they like about it, and what changes they want to see in the future. Filling out the census is a great way to support this project, the wider BOINC community, and have your input heard for future bug bounties. The census is sponsored by the Science Commons Initiative, and the results will be published in an aggregate, anonymized fashion at the completion of the census. Please take 5 minutes to fill out the census at https://app.fillout.com/flow/esDGuRswWfus
17 Nov 2022, 13:24:51 UTC · Discuss
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.
For account creation please use a Crunch_4Science invitation code. It is not needed when registering by BOINC Manager.
Already joined? Log in.
We are going to use donation money for biological evaluation of results.
©2023 SiDock@home Team