Milestones of January
The beginning of the year was productive: 1000 active users and 4000 computers!
With your help, we are finishing the 2nd target, working towards next targets and prospective testing in a wet-lab.
Thanks to everyone and good health.
Hoarfrost and Natalia.
18 Jan 2021, 6:24:36 UTC · Discuss
Second target (corona_PLpro_v1)
Hello everyone! With the beginning of the year, we started processing of the second target, PL Pro. Many new participants joined, so almost half of the library has been docked. Excellent work! Thank you for contributing.
11 Jan 2021, 12:10:19 UTC · Discuss
First target (3CLpro_v3) completion and outage of work
Today we generated the last set of tasks for first target - "corona 3CL pro v3" protein. Also we generated additional set of tasks named like "corona_3CLpro_v3_ext_nb3di_0000493_2_replica". This is replica of tasks that we crunch previously and they need for test purpose - for estimate of possible methods of additional validation of results. In next few days project run out of tasks, but next target and tasks is coming soon!
Thank you for participation and Happy New Year! 2021 is coming!
30 Dec 2020, 22:46:02 UTC · Discuss
CmDock source code
here is the CmDock source code repository: https://gitlab.com/Jukic/cmdock.
This is the main application that we use in the project. Now you can try and build it for your own platforms!
We have many plans and invite C++ devs, especially ones with CUDA and parallel computing knowledge to join our project.
If you would like to join, please contact Marko: jukic (dot) marko (at) gmail (dot) com.
With best wishes,
29 Dec 2020, 8:48:13 UTC · Discuss
Merry Christmas to everyone who celebrates it by the Gregorian calendar! Let it bring joy and love!
We hope you will like the new badges for the total credit. New tasks will be soon. We work at making workflow more stable.
With best wishes, Natalia and hoarfrost.
25 Dec 2020, 7:15:06 UTC · Discuss
This is the production project, a followup to the testing we have been doing. You are welcome to join on our scientific route!
18 Dec 2020, 12:55:33 UTC · Discuss
Transition to production project
During the next few days we plan to transform the current test project into production. Today we generate last bunch of workunits and after its completion test project will go to shutdown. Production project will have another URL and we will publish it. Also we plan to move statistics of teams and participants, as well as accounts information from test to production project.
All of you are highly welcome to stay with us on the production project!
10 Dec 2020, 13:42:35 UTC · Discuss
2020-12-04: progress report
Here is an overview of the work done so far.
Firstly, we have docked 48% of the ligands database to the first target, 3CL Pro. 480 million small molecules were tested in silico. This is a great job! Now we move on to cover 100% of the database.
Virtual screening is a complex procedure that includes post-processing of results, some of them redundant. So the next important step will be processing of the results and studying the chemical subspace they represent. It is important to understand how are the docking scores divided in the dataset. Then our team will develop more efficient filtering rules.
Secondly, the next target for docking is being prepared. Overall, there are 59 targets related to SARS-CoV-2 to investigate.
Thirdly, the new docking software CurieMarieDock has been developed as a fork of RxDock. It is optimised and runs faster. Windows, MacOS and Linux versions are released. ARM version is being prepared.
It is fascinating to work with all of you! Thank you for participating! Have a nice weekend.
With best wishes,
4 Dec 2020, 18:18:08 UTC · Discuss
New application: CurieMarieDock
We are glad to announce the new application CurieMarieDock (cmdock). Currently for Windows 64bit and MacOS 64bit, and more platforms will follow. If you observe errors or undesirable effects in it, please report.
With this application, there is no need for installing MS Visual C++ Redistributable for Visual Studio.
CurieMarieDock is a molecular docking application developed as a fork of RxDock by the authors of the basic COVID.SI project: Marko Jukić, Nejc Ilc, Davor Sluga, Črtomir Podlipnik, and Gašper Tomšič.
Thank you everyone for participating.
2 Dec 2020, 14:25:49 UTC · Discuss
App version 12.2 (Linux 64bit)
Hi all! Please note release of a new Linux version 12.2, the tasks of which the BOINC client should now suspend normally.
Technically, there are two fixes:
1) Wrapper now launches docking application directly, without intermediate script.
2) Wrapper now sends SIGSTOP signal instead of SIGTSTP when suspending a task.
27 Nov 2020, 15:24:02 UTC · Discuss
App version 12.2 (Windows 64bit)
Hi all! Please note release of a new Windows version 12.2, the tasks of which the BOINC client should now suspend normally. Technically, the wrapper now launches docking application directly, without intermediate .bat script.
23 Nov 2020, 15:07:00 UTC · Discuss
App version 12.1 (Windows 64bit)
Please note we released a new app version 12.1 (Windows 64bit). Technically, we deleted the script of calculating task progress which caused many errors. Still, the BOINC client may display task progress using its own algorithms based on the history.
17 Nov 2020, 11:19:46 UTC · Discuss
Disabling task generation for Windows
Dear folks, we temporary disable tasks generation for Windows due to high rate of errors on Windows machines. This application needs more work.
16 Nov 2020, 11:40:05 UTC · Discuss
App version 12.0 (Windows 64bit)
Please note we released a new app version 12.0 (Windows 64bit) which should resolve errors on Windows 7.
16 Nov 2020, 10:53:54 UTC · Discuss
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