News archive

A poll about distributed computing projects
Dear all,

there is a poll created by students who investigate volunteer computing. The questions aim to explore the motivation of participants. If you wish and have a minute, please express your opinion at https://forms.gle/tcLYdtoeVfMMREPE7. The results will be analyzed and presented to the public. Thank you!

With best wishes,
Team of SiDock@home
24 Nov 2021, 11:51:31 UTC · Discuss


Release CmDock v 0.1.4
Dear community. New release of CmDock was prepared. The v0.1.4 of CmDock incorporates fixed checkpointing and progress bar patch along with support for compressed input and output via cmzip. New CmDock release also includes an Updated SDF-Tools submodule that should help the userbase manipulate input/output files with support for large molecular libraries.

Along with the new release, BOINC client is up to date also. The team is working hard and we are committed to support CmDock in the future. Thank You!

Marko & Natalia
21 Nov 2021, 17:10:00 UTC · Discuss


Ninth and tenth targets
Dear participants,

We have a new target which resides at a novel allosteric site on SARS-CoV-2 main protease. The site was identified by MixMD method [1] with collaboration at College of Pharmacy, University of Michigan. Target preparation was helped by Jelena Tošović (Slovenia).

The two upcoming targets and results will complement the allosteric sites identified with X-ray screening by Sebastian Günther et al. [2]. The targets have good chances for wet-lab testing as soon as possible and further experimental support.

(We will again temporarily pause processing of Target 5)

With best wishes,
Team SiDock@home

[1] Phani Ghanakota and Heather A. Carlson. Moving Beyond Active-Site Detection: MixMD Applied to Allosteric Systems. The Journal of Physical Chemistry B 2016 120 (33), 8685-8695. DOI: 10.1021/acs.jpcb.6b03515
[2] Sebastian Günther et al. X-ray screening identifies active site and allosteric inhibitors of SARS-CoV-2 main protease. Science 2021 372 (6542), 642-646. DOI: 10.1126/science.abf7945
13 Nov 2021, 9:39:16 UTC · Discuss


November competition
Dear all,

we are glad to announce a November competition! The symbol of the competition is tryptophan. Just like any amino acid, tryptophan serves as a building block in protein biosynthesis. It is also a source to synthesize serotonin, melatonin, and vitamin B3. And just like many vital processes in our bodies, tryptophan biochemistry is affected by SARS-CoV-2 infection ([1-3] etc.).

1st place:
2nd place:
3rd place:

[1] Thomas T, Stefanoni D, Reisz JA, et al. COVID-19 infection alters kynurenine and fatty acid metabolism, correlating with IL-6 levels and renal status. JCI Insight. 2020;5(14):e140327. Published 2020 Jul 23. doi:10.1172/jci.insight.140327
[2] Eroğlu İ, Eroğlu BÇ, Güven GS. Altered tryptophan absorption and metabolism could underlie long-term symptoms in survivors of coronavirus disease 2019 (COVID-19). Nutrition. 2021;90:111308. doi:10.1016/j.nut.2021.111308
[3] Vyavahare S, Kumar S, Cantu N, et al. Tryptophan-kynurenine pathway in COVID-19-dependent musculoskeletal pathology: a minireview. Mediators of Inflammation. 2021; Article ID 2911578, 6 pages, 2021. doi:10.1155/2021/2911578
28 Oct 2021, 19:08:55 UTC · Discuss


BOINC client 7.16.20 solves the certificate problem for Windows
Dear all,

If you are running BOINC on a Windows computer, please update to a new version (7.16.20) of the BOINC client. The previous version stopped working recently because of an expired SSL file that prevented it from communicating with several BOINC projects, with the BOINC server, and with Science United. You can download the new version here: https://boinc.berkeley.edu/download.php

With best wishes,
Team of SiDock@home
20 Oct 2021, 8:03:32 UTC · Discuss


Certificates and project communicating
Dear folks!

If BOINC on your computer experiencing a problem during project communicating, try to replace file ca-bundle.crt in programs directory of BOINC (C:\Program Files\BOINC\ca-bundle.crt, for example) by this file: https://srbase.my-firewall.org/sr5/download/ca-bundle.crt and restart whole BOINC processes or reboot computer.

Another threads on forum:
Peer certificate cannot be authenticated with given CA certificates
Wus not uploading
Transient Error
Communication deferred
100% block still crunching

Thank you for participation!
4 Oct 2021, 18:55:28 UTC · Discuss


4000 users with credit
Dear SiDockers,

new breakthrough of the project, we will wellcome 4000th user with the credit, very soon.

;-) Crtomir
21 Sep 2021, 15:17:51 UTC · Discuss


SiDock@home September Sailing
Dear participants!

Just now, your computers are hitting three protein targets at once. Due to the low runtimes and (mainly) the friendly contributions of participants and their teams, the data is being processed fast, and we express our gratitude to all of you.
We announce a new competition between teams, SiDock@home September Sailing. Top winners will get the badges:
1st place:


2nd place:


3rd place:


Heme B, the well-known ligand in the complex of Hemoglobin, helps to carry oxygen in our bloodstream. As we know today, it has emerged from just two mutations that occurred in genome of one of predecessors of modern vertebrates more than 400 million years ago [1,2].

[1] https://phys.org/news/2020-05-reveal-complex-hemoglobin-resurrecting-ancient.html
[2] Pillai, A.S., Chandler, S.A., Liu, Y. et al. Origin of complexity in haemoglobin evolution. Nature 581, 480–485 (2020).
12 Sep 2021, 8:19:15 UTC · Discuss


Targets six, seven, eight
Dear participants,

we have prepared three new targets for you! They all base on 3CLpro protein, a prime target for antiviral drug discovery because of its central involvement in virus replication. Another reason to put them high on the list is that we have a good possibility to test interesting results in a lab. The targets 6, 7 and 8 are X-ray identified allosteric sites on 3Clpro. We will make a limited number of workunits to ensure everything works fine, and then launch full-scale screening on the new targets. We will temporarily pause processing of Target 5 in favour of the new ones.

With best wishes,
Team SiDock@home
28 Aug 2021, 16:18:49 UTC · Discuss


Project status: July 2021
Dear all,

Our research is going on! Collaborators just started biological evaluation of 30 chemical compounds selected in SiDock@home for targets 3CLpro and PLpro. Biological evaluation in vitro works with the most prospective results that your computers have selected in silico. The process is iterative and will involve hundreds of experiments.

With your help, we have already processed 4 targets and 43% of the fifth one. Further workunits will be created basing on the biological evaluation and the latest scientific knowledge about the targets.

Many thanks and best wishes,
Team of SiDock@home
9 Jul 2021, 18:21:50 UTC · Discuss


Donations to SiDock@home
Drug development is a time-consuming and costly process. With help of your computers, our team is able to speed up discovery of prospective candidates for in vitro tests. At the same time, the volume of biological evaluation is limited by funding. We are in constant search for additional sources, and, since SiDock@home allows the participants to earn Gridcoins, we find it a good idea to accept voluntary donations. If you feel like donating to the project, please use one of the listed options.
9 Jul 2021, 18:18:53 UTC · Discuss


SiDock@home is whitelisted in Gridcoin
Hello everyone,

since today, SiDock@home is whitelisted in Gridcoin. It means that you can receive the Gridcoin cryptocurrency for contributing to SiDock@home. For instructions, please refer to the official website of Gridcoin. For a description how Gridcoin works, refer to their whitepaper. This technology is yet new to our team, but we will do our best to understand it and help you to use it.
28 Jun 2021, 12:23:44 UTC · Discuss


SiDock@home is going to join Gridcoin
Hello everyone,

we want to be whitelisted in Gridcoin (anytime), so you will be able to receive this cryptocurrency for scientific computing. We believe that Gridсoin is ethical. This is also a chance to increase awareness of the project.
6 Jun 2021, 19:00:14 UTC · Discuss


Release CmDock v 0.1.3
Dear participants!

The following changes will be transparent, but if you are interested in technical details, then here they are. A new application cmdock-boinc-zcp has been released, including the new CmDock v0.1.3 release with (z)ipped input, (c)heckpoints and enhanced (p)rogress bar. In addition, a new docking experiment will begin under a new protocol.

Thanks to the CmDock team and pschoefer & walli for the release!
28 May 2021, 11:07:44 UTC · Discuss


Release CmDock v 0.1.2
Hello everyone,

We are glad to announce the new app version with checkpoints, CmDock v 0.1.2 (cmdock-boinc-zip 2.0 in the BOINC project). Currently it is implemented for Windows 64bit, Linux 64bit and Raspberry Pi (for RPi, please check this thread if you need instructions on configuring the client).

The new release has been tested, but not on every existing computer. In case of any problems, please report.

Thank you all for participation!
20 May 2021, 17:00:11 UTC · Discuss


Half a year, the BOINC Workshop and a move to the new server
Hello all!

Today we celebrate six months of SiDock@home. Thank you for lots of support! Let us summarize the current state:

Science. We are post-processing the obtained results and simultaneously performing virtual screening for the 5th target. With results obtained for several targets, we focus on viral proteases and are in the phase of getting physical samples of compounds for wet-lab testing. We will present the project at the BOINC Workshop on April 28. The event starts at 09:00 PDT / 12:00 EDT / 18:00 CEST / 19:00 EEST, our talk is at +00:40.

Society. The BOINC Pentathlon team selected SiDock@home as this year's Marathon project. The Marathon discipline is announced on 30 April and runs for two weeks from 05 through 18 May.

Technicals. Before the BOINC Pentathlon, we plan to move to a new physical server. The URL will stay the same. But we stop generating tasks and the project will be unavailable for 1-2 days. Also, we are implementing checkpoints as soon as possible.

Best wishes,
SiDock@home team
23 Apr 2021, 10:19:03 UTC · Discuss


BoincWorkshop 2
From chat in BoincWorksop Day 2

"I'm seeing far fewer people interested in running BOINC and many are giving up due to too few "legitimate" projects continuing their research - too many projects have used volunteers and then stopped."

"So, we need more "interesting" projects so people can crunch them...far more people got involved with SiDock, Rosetta and WCG when they launched Covid-19 research tasks..".

Our community is on the right way ;-)

Crtomir
21 Apr 2021, 19:10:17 UTC · Discuss


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




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