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World Community Grid Forums
Category: Completed Research
Forum: Discovering Dengue Drugs - Together - Phase 2 Forum
Thread: [Forthcoming] Live Webcast on DDDT, Dec 6 2013 - Questions for presenters |
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Thread Status: Active Total posts in this thread: 11
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Rickjb
Veteran Cruncher Australia Joined: Sep 17, 2006 Post Count: 666 Status: Offline Project Badges: 
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Copy of the post by ErikaT in the Member News [read only] forum:
December 6th: Upcoming live webcast for Di...ngue Drugs – Together "On December 6th at at 1:00 PM Eastern Time (USA) / 18:00 UTC, Dr. Stan Watowich, of the University of Texas Medical Branch and the principal investigator for the Discovering Dengue Drugs – Together project, will give an overview of the drug discovery process and provide information about the latest steps in his team’s research. Join the webcast to see how the computational results from World Community Grid are helping accelerate the search for important treatments. For more details and the link to join the webcast, read our News & Updates article here ." I will probably not be able to watch/join the forum live at 5am local time, but would like to put some questions to the DDDT scientists: In Phase 1 of the project, the Autodock program was used to screen for drug leads to block critical proteins in the dengue virus and other flaviviridae, but it produced too many false positives to be described as successful. DDDT Phase 2 attempted to address this by re-screening some or all of the compounds using the CHARMM program. Q1: I'm sure that the developers of Autodock at the Olsen lab at TSRI were notified of the failure of Autodock in the DDDT project. Has anyone been able to explain this failure, or at least propose an explanation? Q2: Screening with CHARMM in DDDT2 did not seem to enjoy the hoped-for success either. Has an explanation/proposed explanation been made for this? Q3: VINA is a newer drug-screening program from Olsen at TSRI. Has this been tried against the dengue proteins? In the recent Volume 12 of the FAAH Newsletter is stated (p2): "Since the last newsletter, AutoDock Vina has been implemented on FAAH, .... Due to the rapid computational turn-around, we have decided to now use Vina’s flexible receptor feature." Perhaps trying this for DDDT would produce more useful results. --- Perhaps it is already intended to address some of these issues in the webcast. If not, ... Perhaps others would also like to put questions in advance to the webcast presenters, in which case there's plenty of space for more posts below ... Here's hoping that our questions here will reach the DDDT scientists in time for the webcast. - Rick |
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Dataman
Ace Cruncher Joined: Nov 16, 2004 Post Count: 4865 Status: Offline Project Badges: 
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The webcast was very informative but alas the results-to-date are rather disappointing. Best of luck in future efforts.
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Falconet
Master Cruncher Portugal Joined: Mar 9, 2009 Post Count: 3295 Status: Offline Project Badges: 
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The webcast was very informative but alas the results-to-date are rather disappointing. Best of luck in future efforts. How so? Missed the webcast... 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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littlepeaks
Veteran Cruncher USA Joined: Apr 28, 2007 Post Count: 748 Status: Offline Project Badges: 
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I missed the webcast also -- completely slipped my mind
---------------------------------------- WCG -- will the webcast be posted for us to view? [Edit 1 times, last edit by littlepeaks at Dec 6, 2013 9:18:29 PM] |
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TKH
Former World Community Grid Admin USA Joined: Aug 13, 2005 Post Count: 775 Status: Offline Project Badges: 
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Hi All,
Yes, the webcast will be posted for viewing. We will come back and add the link once it is posted. Thanks. Tedi |
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TKH
Former World Community Grid Admin USA Joined: Aug 13, 2005 Post Count: 775 Status: Offline Project Badges:
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KeithSloan
Cruncher Joined: May 1, 2009 Post Count: 25 Status: Offline Project Badges: 
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The webcast was very informative but alas the results-to-date are rather disappointing. Best of luck in future efforts. How so? Missed the webcast... From memory the results were disappointing as not many compounds were found, and quite a few could be eliminated for other reasons, like toxic to humans etc. But more worrying was that the predictions on compounds that would react with the protein often turned out to be wrong when tested in the Lab. They tried with a second phase and this was not better. In the future they hope to use better docking software. I guess this is all part of the research process, but if the docking software is poor it defeats the object of trying to determine results of chemical reactions via computer simulation.  [Edit 1 times, last edit by KeithSloan at Dec 17, 2013 7:55:32 PM] |
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Viktors
Former World Community Grid Tech Joined: Sep 20, 2004 Post Count: 653 Status: Offline Project Badges:
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Some protein targets are harder to find docking ligands for. They did find some candidates and as it was pointed out, there are many steps before these can become drugs that may be available to the public. Just as another note, we have some researchers that are working on improving the elimination of false positives problem, and this could potentially help this project and others.
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Falconet
Master Cruncher Portugal Joined: Mar 9, 2009 Post Count: 3295 Status: Offline Project Badges:
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Some protein targets are harder to find docking ligands for. They did find some candidates and as it was pointed out, there are many steps before these can become drugs that may be available to the public. Just as another note, we have some researchers that are working on improving the elimination of false positives problem, and this could potentially help this project and others. From a current/past project? 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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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
"We" is IBM researchers, me would bet if I'd bet.
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