Posts by Natalia

41) Message boards : News : BOINC client 7.16.20 solves the certificate problem for Windows (Message 1322) Posted 20 Oct 2021 by Natalia Post: 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
42) Message boards : News : Targets six, seven, eight (Message 1288) Posted 4 Oct 2021 by Natalia Post: We aim to release a version for Mac OS, hopefully soon.
43) Message boards : News : SiDock@home September Sailing (Message 1141) Posted 12 Sep 2021 by Natalia Post: 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).
44) Questions and Answers : Web site : SiDock's parent site not working (Message 1131) Posted 3 Sep 2021 by Natalia Post: Thank you for the notice, they solved the problem.
45) Message boards : News : Targets six, seven, eight (Message 1119) Posted 30 Aug 2021 by Natalia Post: Are those targets solved by AlphaFold already? How to compare Sidock to AlphaDock ? the AlphaFold project aims at predicting three-dimensional shapes of proteins in silico (in a computer). The results can be very useful indeed, but one needs additional information to do virtual screening. In particular, one needs to determine the potential binding site on the complex surface of the protein. Our new targets are such binding sites identified in a recent paper. The authors studied the protein as a crystal using X-rays rather than in silico.
46) Message boards : News : Targets six, seven, eight (Message 1115) Posted 28 Aug 2021 by Natalia Post: 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
47) Questions and Answers : Windows : I have problems with project in my network (Windows 7 with extendent support) (Message 1086) Posted 11 Jul 2021 by Natalia Post: It's great that the problem is solved! Now we will know if other people face the same problem.
48) Message boards : News : Project status: July 2021 (Message 1082) Posted 9 Jul 2021 by Natalia Post: 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
49) Message boards : News : Donations to SiDock@home (Message 1081) Posted 9 Jul 2021 by Natalia Post: 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.
50) Message boards : News : SiDock@home is whitelisted in Gridcoin (Message 1078) Posted 9 Jul 2021 by Natalia Post: LennStar, thank you for the nice explanation! Our team is also new to Gridcoin.
51) Message boards : News : SiDock@home is whitelisted in Gridcoin (Message 1056) Posted 28 Jun 2021 by Natalia Post: 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.
52) Message boards : News : Upcoming conference: ANTYCOVID-21 (online) (Message 1051) Posted 25 Jun 2021 by Natalia Post: The conference starts on Monday, June 28th, online, 10.00 (CET time). The talks will present IT solutions in the fight against Covid-19. We are glad that our talks were accepted: 1) 10:15 (CET time) Marko Jukić. Bioinformatic and MD analysis of N501Y SARS-CoV-2 (UK) variant 2) 10:35 (CET time) Natalia Nikitina. Volunteer computing project SiDock@home for virtual drug screening against SARS-CoV-2 The conference program and the link to Zoom meeting are available.
53) Message boards : Science : Visualisation of molecular docking performed (Message 1048) Posted 22 Jun 2021 by Natalia Post: This video, prepared by Dr. Jukić and Dr. Podlipnik, shows a bit of modeling performed by your computer for SiDock@home. A small molecule (moving one) tries to dock to the target molecule (fixed one, with a gray surface). The aim is to find a pose with the best binding energy. This process is somewhat similar to putting a key into a lock. Millions of "keys" are being checked, and for each one, the best binding pose is predicted. This is how virtual drug screening works, and a big work on results post-processing is ahead.
54) Message boards : News : SiDock@home is going to join Gridcoin (Message 1022) Posted 6 Jun 2021 by Natalia Post: 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.
55) Message boards : News : SiDock@home becomes a general drug discovery project (Message 1003) Posted 1 Jun 2021 by Natalia Post: Thank you for useful advice! We don't have much experience with Twitter yet.
56) Message boards : News : Release CmDock v 0.1.3 (Message 999) Posted 31 May 2021 by Natalia Post: We are unable to reproduce the error at our side, but will be aware. Could it be a lack of disc space?
57) Message boards : Number crunching : Mac SiDock (Message 998) Posted 31 May 2021 by Natalia Post: Hello! We are still working on MacOS version v0.1.3.
58) Questions and Answers : Unix/Linux : Please provide an app for Raspberry Pi (GNU/Linux / ARM64) (Message 997) Posted 31 May 2021 by Natalia Post: Hello! Have you altered cc_config.xml as discussed above?
59) Message boards : News : SiDock@home becomes a general drug discovery project (Message 996) Posted 31 May 2021 by Natalia Post: Hello! A great idea, here it is: https://twitter.com/SiDockProject.
60) Message boards : News : Release CmDock v 0.1.3 (Message 979) Posted 28 May 2021 by Natalia Post: 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!

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