1) Message boards : Cafe : Greetings from Sweden! (Message 2145) Posted 20 Nov 2023 by Marko Jukic Post: Thank You! All the best.

2) Message boards : Number crunching : Gpu app? (Message 2144) Posted 20 Nov 2023 by Marko Jukic Post: Dear member, Yes, the tasks are long due to target specifications. In the future, we will tailor the tasks to be shorter. Regarding GPU, we are working hard to bring GPU support to CmD. We are very close now, nevertheless, it really took us by surprise how much effort it is. Good luck to us all, and let's go on! Marko

3) Message boards : News : Target 21: corona_TMPRSS2_v1 (Message 1792) Posted 9 Jan 2023 by Marko Jukic Post: Dear SiDock@home community, We are grateful for your interest! Indeed, TMPRSS2, or transmembrane protease, serine 2 is a protease on host cells. In contrast to targeting viral proteins, herein, we target a host protein (host-directed approaches) that is responsible for viral Spike protein processing and, ultimately, viral entry into host (our /human) cells. The potential inhibitor compounds herein could hinder viral entry and be useful as probes for viral studies. Some non-selective compounds are already known, but additional insights are welcome. Thank You All !!! Marko p.s. We are still delving into SARS-CoV-2 due to future work, however, in the future of SiDock@home, expect also other targets to be investigated in this wonderful drug design community project. p.p.s. Thanks also, Aurum for the help and the link to the article: Nature Reviews Molecular Cell Biology volume 23, pages 3–20 (2022). Also, some excellent work herein: Nature volume 605, pages340–348 (2022).

4) Message boards : News : Release CmDock v 0.2.0 (Message 1775) Posted 14 Dec 2022 by Marko Jukic Post: Dear SiDock@home community, CmDock 0.2.0 is released: -Cross-platform consistent random number generator (custom implementation of probability density functions); new switch -x defined, which turns on this feature. -CI pipeline with regression testing -logging in cmcavity -cmcavity implementaiton of cavity volumes in InsightII (-I) or MRC 2014 (-M) -Full protein surface mapping -Pymol GUI plugin for Your demo/teaching/visualisation/research projects ;) You can get it at: https://gitlab.com/Jukic/cmdock/ Happy holidays to all! , and all health! Marko & CmDock team & SiDock@home team

5) Message boards : News : CmDock new release pending (Message 1774) Posted 14 Dec 2022 by Marko Jukic Post: Dear SiDock@ home community, It has taken us some additional time but CmDock 0.2.0 is released. https://gitlab.com/Jukic/cmdock/ Check the release thread. Marko

6) Message boards : News : CmDock new release pending (Message 1752) Posted 10 Nov 2022 by Marko Jukic Post: Dear SiDock@home community, Indeed it was a while longer, but we are releasing CmD v.0.2.0 in the next 1-2 weeks. We are happy with the improvements and as it stands, this is hopefully planned as the last CPU-only CmD release. let's go on! Marko Jukic

7) Message boards : News : Donations to SiDock@home (Message 1751) Posted 10 Nov 2022 by Marko Jukic Post: Dear Jay, Thanks for the heads up. It should be fixed and working in 24 h. We are so thankful for all the help! You and the whole community keep us going! All the best and all health! Marko

8) Message boards : News : CmDock new release pending (Message 1688) Posted 11 Aug 2022 by Marko Jukic Post: @cybertailor, Indeed, as You well know. @captain crunch. No, it will be automated via BOINC. This is for users who wish to use CmD in their research and can conveniently use homebrew. @speedy51. We are working in the background on OpenCL implementation. The work is hard, to say the least. We are in desperate need of contributors and also financing ... We will release another CmD 0.1.5 end of September (we wish) and expect to have the first version of GPU committed after that ... (we wish) ...

9) Message boards : Cafe : Russia and Ukraine (Message 1684) Posted 7 Aug 2022 by Marko Jukic Post: Dear all, no governments are involved in this purely scientific project. All the software is established and open source! All the best! CmDock team

10) Message boards : Number crunching : Target 17: corona_Eprot_v2; Target 18: corona_Eprot_v3 (Message 1675) Posted 22 Jul 2022 by Marko Jukic Post: Yes, as discussed in the June post, we are staying on SARS-CoV-2 on demand.". We are studying SARS-CoV-2 E protein, however, in general, our protein systems are robust regarding viral variants and hit compounds would be expected to be active on a plethora of viral variants.

11) Message boards : News : CmDock new release pending (Message 1674) Posted 22 Jul 2022 by Marko Jukic Post: Dear SiDock@home community, Just a little update on the development of our CmD software. We were planning to release CmD 0.1.5.; however, we decided to wait a bit. Namely, we want to implement a robust testing (regression, unit) pipeline and lay the work for future software optimization. Therefore we would like to implement a cross-platform consistent pseudo-random number generation that would mean - write once, compile and test everywhere... We think this can be achieved relatively quickly. On the other front, Mac builds are being tested and we will provide the community with Mac builds through homebrew platform. We will publish the news on future release here. All the best, Marko

12) Message boards : News : Project status: May 2022 (Message 1649) Posted 15 Jun 2022 by Marko Jukic Post: Dear SiDock@home community, This international scientific drug discovery project is going diligently on! with respect to our previous target study plans, there were some alterations from the plan published in Project status: March 2022. Namely, after nsp14 we continued with SARS-CoV-2 targets. We are studying allosteric binding sites on SARS-CoV-2 3CLpro and PLpro proteases due to engaging results and collaboration towards further illuminating 3Clpro and PLpro drug design potential. Sadly this pathogen causes global health problems and is still of grave concern. However computational engagement on these studies are coming to an end and we are turning our attention toward therapeutic targets of the Ebola viral pathogen to return back to SARS-CoV-2 on demand. Your support keeps us going and thank You again SiDock@home community !!! All health, luck, and Peace to all! Marko Jukic

13) Message boards : News : Project status: March 2022 (Message 1648) Posted 15 Jun 2022 by Marko Jukic Post: Dear SiDock@home community, This international scientific drug discovery project is going diligently on! with respect to our previous target study plans, there were some alterations from the plan published in Project status: March 2022. Namely, after nsp14 we continued with SARS-CoV-2 targets. We are studying allosteric binding sites on SARS-CoV-2 3CLpro and PLpro proteases due to engaging results and collaboration towards further illuminating 3Clpro and PLpro drug design potential. Sadly this pathogen causes global health problems and is still of grave concern. However computational engagement on these studies are coming to an end and we are turning our attention toward therapeutic targets of the Ebola viral pathogen to return back to SARS-CoV-2 on demand. (will repost in project status May.) Your support keeps us going and thank You again SiDock@home community !!! All health, luck, and Peace to all! Marko Jukic

14) Message boards : News : Project status: March 2022 (Message 1570) Posted 14 Mar 2022 by Marko Jukic Post: Dear SiDock@home community, Here is an update on our work. This international scientific drug discovery project is well on its way towards its first milestone of experimental support for the docked compounds. We are working hard towards data processing and scientific collaborations that can help us take our proposed compounds further. In the near future, we will prepare a scientific write-up for You to follow. This international drug discovery project is a wonderful example of community, citizen science, teamwork, and contributing to the field of medicinal chemistry with the ultimate goal of contributing to the wellbeing of us all. Our heart goes out to all! We also thank You for the help and support that keeps us going. Currently, our servers reside in Russia and Slovenia. This enables us easier task allocation and backup of the results and we hope to add a third location with additional hardware in the future. Due to the community request, we also plan to add official Mac and ARM64 support for the underlying CmDock software. Moreover, we are continuing with a new target, still from the SARS-CoV-2 pathogen, namely nsp14. It consists of the N-terminal ExoN domain involved in proofreading and the C-terminal guanine N7 methyl transferase (N7-MTase) domain that functions in mRNA capping and on the latter we are focusing on now. After this target is complete, we are turning our attention towards one potential therapeutic target of the Ebola viral pathogen to return back to SARS-CoV-2 after that target will be complete. We are committed to this drug discovery project and the online community, hope to expand and we look forward to working and discovering new molecules and compound mechanisms of action in the future. All health, luck, and peace to all! Marko Jukic

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