Posts by Natalia

21) Questions and Answers : Windows : Project fills CPU use to 100% although "Use at most xx% of CPU time" is set (Message 1564) Posted 9 Mar 2022 by Natalia Post: Hello! Regarding the images, you insert them correctly. The problem seems to be in the hosting you are using.
22) Message boards : News : Technical maintenance on February 14th (Message 1486) Posted 11 Feb 2022 by Natalia Post: Dear all, On February 14th, for about 08:00-20:00 UTC, the project server will be shut down for maintenance. We will upgrade hard drives to support larger loads. All the best, Team SiDock@home
23) Message boards : News : Target 11 - Sprot_delta_v1 (Message 1485) Posted 10 Feb 2022 by Natalia Post: Dear Participants, We continue diligently with the calculations. Now we are breaking through a series of protease studies to explore a new target, the RBD (receptor-binding domain) Sprot domain surface interacting with ACE2. This is the much-discussed spike protein that also contributed to the naming of coronavirus. We focus here on Sprot from the delta variant (B.1.617.2), specifically a Cryo-EM structure of Sprot with an RBD in up conformation. In comparative variant studies, we will try to determine if there is a specific discrimination upon binding of small ligands. This may help us better understand this PPI surface in further studies and even develop a small molecule probes to study these interactions. Thank You all and we look forward to future studies together! With best wishes, Team SiDock@home
24) Questions and Answers : Macintosh : No new Workunits for MacOS? (Message 1476) Posted 24 Jan 2022 by Natalia Post: We aim to enable an app for Mac. No exact dates though. We are sorry it has extended for so long, but this is nothing we can do immediately.
25) Message boards : Cafe : Comparison to other projects? (Message 1467) Posted 22 Jan 2022 by Natalia Post: Hi Jay! You are welcome to the project SiDock@home! Let me describe the difference between the projects. Just like WCG - Open Pandemics, in SiDock@home we perform virtual screening over a database of small molecules. Each WU performs molecular docking of a small part of the library against a specified target. Targets are various proteins of SARS-CoV-2. However, the molecular docking software is different (AutoDock Vina in WCG, CmDock in SiDock@home, both open-source and actively developing). The sets of targets are also different but can be partly intersecting because the scientific community prioritises some of them as the most important. The databases of small molecules are also different because each scientific group compiles them based on their previous experience. In Rosetta@home, the scientists analyse the folded proteins, including those of SARS-CoV-2. They also perform protein-protein docking, which means they explore how specially designed proteins dock to the target proteins. As far as I know, they also molecular docking but, again, for different targets, software and the database of small molecules. I hope it explains the difference between the projects.
26) Message boards : Cafe : 12. CHARITY EVENT 2022 (Message 1448) Posted 11 Jan 2022 by Natalia Post: I see the idea as follows. The Charity Team attracts volunteers to contribute computational power during two weeks. This boosts the project's progress, and also promotes the knowledge about the project in the BOINC community. It is comparable with various charity sport events where participants make effort to raise funds rather than compete for one's own rating. We (the team of SiDock@home) are very grateful for being selected this year.
27) Message boards : Number crunching : [Guide][Linux] Running SiDock@home tasks for CmDock on anonymous platform (Message 1427) Posted 28 Dec 2021 by Natalia Post: Note: if you use CmDock v0.1.4 (the latest at the moment), step 6 should read: 6. Create empty file docking_out
28) Message boards : News : Merry Christmas! (Message 1403) Posted 26 Dec 2021 by Natalia Post: Dear participants, Merry Christmas and a happy New Year to all of you! We wish you lots of health, love and joy. With Your help, we have done an enormous research work, and we are preparing to do even more and take this drug discovery project even further. We will be tackling future key problems in drug design and are working hard to overcome all obstacles of financing (with your help it is easier… thank You all!!!) and wet lab support! Currently, we are finishing the 5th target and also returning to 3CLpro allosteric sites towards further in depth research. All the best! From Natalia, Marko, Črtomir and hoarfrost
29) Message boards : Number crunching : A challenge of December 2021 (Message 1402) Posted 26 Dec 2021 by Natalia Post: A technical issue. Due to a technical error, some tasks run normally, but are reported as failed. If convenient, please abort the following tasks on your computers: app version 2.01, id<=380000, suffix _0 or _1. For example: a task corona_Eprot_v1_run_2_nb3di_377447_3_1 should be aborted. We are very sorry for this issue and hope it will not bring too much bother.
30) Message boards : Number crunching : A challenge of December 2021 (Message 1396) Posted 20 Dec 2021 by Natalia Post: Dear all, A new challenge has been announced! It will help us to proceed on the 5th target with its long-running tasks. The event starts on December 24 08:45 UTC, ends on December 31 08:45 UTC. All teams are welcome to participate! We prepared special badges for the winners. They depict a molecule of leucine, an essential amino acid. Leucine contributes to the regulation of blood-sugar levels, growth and repair of muscle and bone tissue, growth hormone production and wound healing. Leucine also prevents breakdown of muscle proteins after trauma or severe stress. The name of the compound comes from Greek, λευκός (leukos, "white"). A nice reason to put it as a reward for the December competition!
31) Message boards : Number crunching : lots of tasks error out suddenly (Message 1378) Posted 6 Dec 2021 by Natalia Post: Could you specify the computer please? I see several computers belonging to you in the database, there are some error results, but some of them seem to have been resolved.
32) Message boards : News : A poll about distributed computing projects (Message 1371) Posted 24 Nov 2021 by Natalia Post: 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
33) Message boards : News : Release CmDock v 0.1.4 (Message 1368) Posted 21 Nov 2021 by Natalia Post: 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
34) Message boards : News : Ninth and tenth targets (Message 1363) Posted 20 Nov 2021 by Natalia Post: Update: the 10th target goes in a tight bundle with the 9th :)
35) Message boards : News : Ninth and tenth targets (Message 1353) Posted 13 Nov 2021 by Natalia Post: 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
36) Message boards : News : Donations to SiDock@home (Message 1337) Posted 1 Nov 2021 by Natalia Post: Hi walli, thank you for the notice! I changed the path.
37) Message boards : News : November competition (Message 1333) Posted 28 Oct 2021 by Natalia Post: 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
38) Message boards : News : Donations to SiDock@home (Message 1332) Posted 28 Oct 2021 by Natalia Post: How many $/€/GRC do you need to evaluate a single compound? My hunch is that this is below $/€1000, which should be in reach for individual teams to fund - would you give medals for that? The question about the cost of biological evaluation is very complex as it includes the cost of compounds themselves as well as researcher time with lab supplies (assay cost) and all equipment. But your hunch is good and current in vitro enzyme inhibition assays are well achievable: Single compound costs range from 50 to cca 100 € per compound "in stock" with up to 200 € for "on demand" compounds. Together with everything, we would estimate the average costs per single compound reside around 100-150 €. Nevertheless, we aim towards additional cell and SPR assays in the future and that will bring us additional costs as well as accompanying analytics on the compounds (MS, NMR, HPLC). That will be done only for the best hits so we are not afraid of the future! We are focused on finding good compounds and bringing new information to the field! Marko Jukić and Natalia Nikitina, on behalf of the team.
39) Questions and Answers : Web site : How often SiDock@home statistics updated? (Message 1331) Posted 28 Oct 2021 by Natalia Post: How often are the SiDock@home team and individual participant statistics updated? How often are SiDocks stats available to other statistic websites? Every hour, day, other? Thank you. Hello! I don't remember changing the default setting, and I see that stats are updated every 4 hours.
40) Message boards : News : Donations to SiDock@home (Message 1330) Posted 28 Oct 2021 by Natalia Post: How many $/€/GRC do you need to evaluate a single compound? My hunch is that this is below $/€1000, which should be in reach for individual teams to fund - would you give medals for that? Incorporation of the personal donations into the workflow is a great idea, we will do our best for it.

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