21) Message boards : Science : Other uses of docking than viruses? (Message 766) Posted 3 Apr 2021 by Crtomir Post: Dear Jim, molecular docking is method of structure based drug design, and is not limited only for screening for antiviral compounds. Docking is useful for all problems where we know high resolution structure of the target (usually proten, but could be also dna or rna). We will explore in the future also other targets than for corona; that would be not neccessarly connected with viruses. In future we will search also for antimalarics and other tropical neglected diseases, therapeutics against dementia, obesity, etc. All the best, Crtomir

22) Message boards : Number crunching : No checkpoints? (Message 751) Posted 26 Mar 2021 by Crtomir Post: Dear Crunchers, it seems that the E protein is a very specific target, and HTVS (High Throughput Virtual Screening) for some WU do not find a pose of the ligand within the receptor. We can think of our experiment as sieving, where the composition of the fractions depends on the choice of sieve. Perhaps our standard sieve has oversized pores and sometimes the fraction on the sieve contains no particles. We still hope to find between one billion molecules, some potential inhibitors of protein E. Crtomir

23) Message boards : Cafe : Whitelist SiDock for Gridcoin - What say ye? (Message 732) Posted 23 Mar 2021 by Crtomir Post: Dear fellow members of the Boinc community, I'm pleased to announce that the core group of the SiDock@Home project approved GridCoin idea, but we need some time to prepare our servers and also to set up checkpoints (important task in our priority list). We estimate that we will be ready to launch GridCoin in two months. What are next steps. Crtomir

24) Message boards : News : Fifth Target is SARS-CoV-2 EProtein (Message 655) Posted 19 Mar 2021 by Crtomir Post: 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 ;-)

25) Message boards : Science : Ask me a question? (Message 625) Posted 28 Feb 2021 by Crtomir Post: The file with extension .mol2 carries structural information of the protein (targets), while .sdf files are for ligands, in one sdf file you can find many ligands separated by $$$$. Yes, you can produce mutants but it is not so simple, the best way to do this is using SWISSMODEL https://swissmodel.expasy.org/, you need sequence of the protein written in fasta and the template in pdb for example ( https://www.rcsb.org/structure/6M71 ).

26) Message boards : News : Fourth target (corona_RdRp_v1) (Message 600) Posted 17 Feb 2021 by Crtomir Post: Dear SiDock@Home supporters, the 4th target will soon be in use ;-). In the first three sessions of the project (the first three targets), we have produced a large amount of data (tens of TB) . Working with BIG data is a great challenge for us, without your help we would not have been able to study a large part of the chemical space. The big data we produced together is a very big treasure for us. I would like to take this opportunity to thank all the supporters who donate their computing power to help us in the project to fight SARS-CoV-2. We hope to find at least some promising compounds in the project that are suitable for the development of inhibitors of processes that are crucial for the functioning of the virus. Crtomir

27) Message boards : Number crunching : BOINCstats BAM challenge has been called on your project (Message 594) Posted 12 Feb 2021 by Crtomir Post: Natalia did a really nice presentation about our project: https://www.youtube.com/watch?v=RcSoS8q8oWc&feature=share ;-)

28) Message boards : Cafe : Whitelist SiDock for Gridcoin - What say ye? (Message 589) Posted 11 Feb 2021 by Crtomir Post: Gridcoin. Good idea ;-). Do you have experience how to set this. Crtomir

29) Message boards : Number crunching : BOINCstats BAM challenge has been called on your project (Message 588) Posted 11 Feb 2021 by Crtomir Post: Excellent !!! With this power we can screen 1 B compounds in one week. This is impressive.

30) Message boards : Number crunching : BOINCstats BAM challenge has been called on your project (Message 584) Posted 10 Feb 2021 by Crtomir Post: Server will survive, and we already docked more than 800 M compounds to PLPro target. I am proud that I am part of this project. Crt

31) Message boards : Number crunching : BOINCstats BAM challenge has been called on your project (Message 558) Posted 6 Feb 2021 by Crtomir Post: Already > 20 000 Gigaflops, and server is still allive ;-)

32) Message boards : Number crunching : BOINCstats BAM challenge has been called on your project (Message 557) Posted 6 Feb 2021 by Crtomir Post: Hello Alez, my teamate ;-) Cheers

33) Message boards : News : Release CMDock v 0.1.1 (Message 554) Posted 6 Feb 2021 by Crtomir Post: Boinc was our first choice in the beggining of the COVID.SI project, but unfortunately no one from core team had knowledge to setup Boinc server properly. So we developed own server client system that is on duty almost one year. There is not so many information for users but system: https://covid.si/en/quick-start/ is working. We already screened more than 10 M ligands to 60 targets related to SARS CoV 2. The sistem that we sat is lighweight but in future we can include some credit system to motivate users, this require login system (this is not big issue) with GDPR compilance. Dealing with users data is very delicate and in Slovenia we have huge penalties is something goes wrong. We will not retire our system, we decided to use it for boutique projects. Since the system is json configured we can screen small subsets of whole database to specific target. After months of running server/client system on Covid.si we meet an excellent team from Petrozavodsk, Karelia, Russia, which helped us to set up Boinc server for the project, even more they offer us full support and now Natalia and her collaborators are part of COVID.SI core group. Together we are stronger ;-)

34) Questions and Answers : Macintosh : Work units for Mac (Message 549) Posted 6 Feb 2021 by Crtomir Post: Dear MAC users, currently we have not official apple developer account, thus we can not issue mac version. If some one has idea to help us to solve this issue please contact jukic dot marko at gmail dot com ;-)

35) Message boards : News : Release CMDock v 0.1.1 (Message 548) Posted 6 Feb 2021 by Crtomir Post: In my oppinion Is the same product. Maybe little inconsistence in naming. I will ask main developer M. Jukic about differences between them. The best of all is that you can downoad software for using in own chemoinformatics and drug design problems. All the best Crtomir

36) Message boards : News : Release CMDock v 0.1.1 (Message 540) Posted 5 Feb 2021 by Crtomir Post: Official release of CurieDock (CMDock v 0.1.1) for windows, linux and arm (raspberry pi): https://gitlab.com/Jukic/cmdock/-/releases

37) Message boards : Number crunching : Server acting up (Message 521) Posted 5 Feb 2021 by Crtomir Post: The project getting bigger and bigger. We need to set new servers soon.

38) Message boards : Number crunching : BOINCstats BAM challenge has been called on your project (Message 519) Posted 5 Feb 2021 by Crtomir Post: Nice run. We are at Current GigaFLOPS 18775.44 (new record), and server is still alive ;-)

39) Message boards : News : Temporary task shortage (Message 466) Posted 26 Jan 2021 by Crtomir Post: Note on validation of docking results: Molecular docking is an optimization process in which we search for the position of a molecule within the receptor site of a protein by maximizing the number and strength of favorable contacts and the number and strength of unfavorable contacts. CMDock (RXDock) uses a combination of two stochastic algorithms (Genetic Algorithm and Monte Carlo) to perform the docking. Due to the stochastic nature of the molecular docking process, it is impossible to get exactly the same output for different runs of the input. This is also the reason why only one run per molecule is not sufficient to obtain a picture of the protein-ligand interaction. In case of Molecular Docking validation is not straightforward ;-)

40) Message boards : News : Milestones of January (Message 426) Posted 18 Jan 2021 by Crtomir Post: My dear colleagues Natalia and Hoarfrost You are doing an excellent job. We will soon finish the second target SARS-CoV-2 PL -Pro as well. I hope for exciting results ;-) All the best! Crtomir

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