News archive

Upcoming conference: ANTYCOVID-21 (online)
Dear all,

on June 28-29 2021, there will be a scientific conference "ANTYCOVID-21: Computer science protecting human society against epidemics", in an online format, hosted in Poland. We aim to present a talk about SiDock@home and will be glad to see all of you as listeners. We also encourage you to submit own works if you participate in a covid-related research!

Conference leaflet

Dates:
Paper submission 15 April 30 May (extended)
Notification of paper acceptance: 15 May
Final paper submission and registration: 30 May
Conference 28-29 June 2020

Submissions:

The papers should be submitted via Easychair
The submission may include long papers limited to 12 pages in Springer LaTex llncs format or short papers (up to 4 pages)
All questions about submissions may be emailed to antycovid21 at easychair.org
2 Apr 2021, 11:27:23 UTC · Discuss


Fifth Target is SARS-CoV-2 EProtein
Our fifth target is the E protein. We are emotionally attached to this protein because we explored its druggability in the early days of our project in the context of Covid.

At only 75 amino acids long, the envelope protein (E) is the smallest of the four structural proteins that make up the SARS-CoV-2 virus particle, and it is essential for the virus to infect cells. Data from other coronaviruses led researchers to suspect that groups of five E proteins form a pore that spans the lipid bilayer membrane of the virus. However, there was no direct evidence because the structural characterization of membrane-spanning proteins is difficult with the most commonly used techniques - X-ray crystallography and cryo-electron microscopy. Mei Hong's group at the Massachusetts Institute of Technology instead used nuclear magnetic resonance spectroscopy to solve the structure of the E protein and confirm pore formation (Nat. Struct. Mol. Biol. 2020, DOI: 10.1038/s41594-020-00536-8). The group also investigated how two drugs, amantadine, and hexamethylene amiloride, can bind to and block the pore. Although these drugs only bind weakly to the pore, the researchers say the new structural information could help in the development of drugs that target the virus.

In our HTVS, we will screen 1 billion of the small molecules to the pore of the E protein pentamer. We hope to find some nice molecules that can block the pore ;-)
19 Mar 2021, 21:50:22 UTC · Discuss


SiDock@home becomes a general drug discovery project
Hello everyone!

We are happy to announce that SiDock@home will continue as a general drug discovery project, not limited to coronavirus only! This means that the project will continue for a long time. We aim to develop and incorporate novel methods of drug design and perform drug discovery for different diseases.

Nevertheless, the first mission on fighting the coronavirus continues! There are many results to process and more targets to explore within what started from COVID.SI project.

With best wishes,
Natalia and the team.
27 Feb 2021, 14:06:38 UTC · Discuss


Fourth target (corona_RdRp_v1)
We are glad to announce the fourth target, corona_RdRp_v1. This molecule is frequently used in research studies as a potential target to inhibit viral replication. Specifically, it is SARS-CoV-2 RNA-dependent RNA polymerase (RdRp in short), an enzyme which coronavirus SARS-CoV-2 uses for the replication of its genome and the transcription of its genes.
8 Feb 2021, 8:17:30 UTC · Discuss


Release CMDock v 0.1.1
Official release of CurieDock (CMDock v 0.1.1) for windows, linux and arm (raspberry pi):

https://gitlab.com/Jukic/cmdock/-/releases
5 Feb 2021, 19:10:12 UTC · Discuss


Third target (corona_PLpro_v2)
Hello everyone!

We are glad to announce work on the third target: PLpro_v2, the same protein with another catalytic active site.
We resume task generation with a new validator. It was implemented to automate result check which caused some delays before.

Thank you all for supporting the project!
29 Jan 2021, 10:21:40 UTC · Discuss


Temporary task shortage
Hello everyone! There is a temporary task shortage due to finishing the 2nd target, moving to the 3rd one and improving the docking protocol. Thank you for your patience!
21 Jan 2021, 15:30:02 UTC · Discuss


Milestones of January
Hello everyone!

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
Hi folks!

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
Hi everyone,

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,
Natalia
29 Dec 2020, 8:48:13 UTC · Discuss


Merry Christmas!
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


SiDock@home
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
Hi folks!

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
Hello everyone!

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,
Natalia
4 Dec 2020, 18:18:08 UTC · Discuss


New application: CurieMarieDock
Hello everyone!

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




News is available as an RSS feed   RSS

©2021 SiDock@home Team