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World Community Grid Forums
Category: Active Research
Forum: OpenPandemics - COVID-19 Project
Thread: Developing ZINC Thread maybe adressed mainly to the researchers and their collegues from other universities |
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Thread Status: Active Total posts in this thread: 6
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Martin Schnellinger
Advanced Cruncher Joined: Apr 29, 2007 Post Count: 123 Status: Offline Project Badges: 
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I understand, that what we are doing here is the following:
Our machines use the ZINC database, which is in simple words a list of substances. The machines take one subtance, compare its chemical parameters to the parameters of a molecule of the virus. Then they have a look a the next chemical substance, compare the parameters and so on. Maybe in reality it is more complicated, but let us say it in this way. I wonder whether it would make sense to publish the criteria, why a certain subtance is listed in ZINC. Why has this or that subtance been chosen to be part of ZINC? What are the plans for the next version of ZINC? Which subtances will be added, and for which reason these substances and not others? A hard question, sorry, but it might contribute to develoop ZINC. I am not a chemist, I will not be able to be active, but mabe there are chemists/biolgoists/pysicans here who could give valubale hints for good candidats to become part of ZINC? Thank you for any comments or good advice in which direction to go. |
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Falconet
Master Cruncher Portugal Joined: Mar 9, 2009 Post Count: 3295 Status: Offline Project Badges: 
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These questions may have their answers on the ZINC website.
----------------------------------------Wikipedia has this: "ZINC is different from other chemical databases because it aims to represent the biologically relevant, three dimensional form of the molecule." I'm not a chemist or researcher but sounds like they only list biologically active molecules, so I'm guessing only molecules that can play a role on an organism. As for the rest of your questions, again, check the ZINC website since ZINC doesn't really have anything to do with the OPN researchers. AMD Ryzen 5 1600AF 6C/12T 3.2 GHz - 85W AMD Ryzen 5 2500U 4C/8T 2.0 GHz - 28W AMD Ryzen 7 7730U 8C/16T 3.0 GHz [Edit 2 times, last edit by Falconet at May 6, 2021 3:38:15 PM] |
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Martin Schnellinger
Advanced Cruncher Joined: Apr 29, 2007 Post Count: 123 Status: Offline Project Badges:
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Hello Falconet,
may I cite you "since ZINC doesn't really have anything to do with the OPN researchers." Please check the log of any OPN workunit. There you will find that ZINC is written in the log. This means logically, that ZINC must be the basis of OPN. Please look This is a log of a OPN workunit, done by my machine <core_client_version>7.2.47</core_client_version> <![CDATA[ <stderr_txt> INFO:[12:12:17] Start AutoGrid... autogrid4: Successful Completion. INFO:[12:12:32] End AutoGrid... INFO:[12:12:33] Start AutoDock for ZINC000492318213_RX1 --fr824_001--CYS114_wcgsplit2.dpf(Job #0)... You see the name ZINC marked in red. This is where the workunit is "linked" to the database ZINC. There Is no other reason why they would mention ZINC in the workunit but the fact, that ZINC is the basis of OPN Thank you for disussing, falconet. Best MS |
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caitilarkin
Former World Community Grid Admin USA Joined: Nov 4, 2015 Post Count: 331 Status: Offline Project Badges: 
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The OpenPandemics - COVID-19 researchers have posted the scientific details of the project on their website. They've also discussed the details of the molecules they're studying on our website .
----------------------------------------ZINC is a widely used scientific database from which the researchers are choosing molecules. The people and organizations who are involved in determining which molecules are chosen and how they are chosen are listed in the About section of the ZINC website. They would be able to address your questions. [Edit 1 times, last edit by caitilarkin at May 6, 2021 5:33:52 PM] |
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Martin Schnellinger
Advanced Cruncher Joined: Apr 29, 2007 Post Count: 123 Status: Offline Project Badges:
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Thank you very much, caitilarkin.
Looks like I will have to use the general e-mail of the University of California. Since Questions, Discussion, Bug reports, Feature requests on the page https://zinc.docking.org/ Gives the result Not Found The requested URL /forum/14 was not found on this server. Seems as if they do not want to get e Mails. Well, everyone has the right to keep e Mail not public Thank you anyway. MS |
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Falconet
Master Cruncher Portugal Joined: Mar 9, 2009 Post Count: 3295 Status: Offline Project Badges:
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I meant that they simply use the ZINC Database. They don't manage it.
----------------------------------------ZINC is used by many researchers around the world. The ZINC code you see there corresponds to a molecule. You can copy it and go the ZINC database to find out more details about that molecule. AMD Ryzen 5 1600AF 6C/12T 3.2 GHz - 85W AMD Ryzen 5 2500U 4C/8T 2.0 GHz - 28W AMD Ryzen 7 7730U 8C/16T 3.0 GHz |
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