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World Community Grid Forums
Category: Completed Research
Forum: FightAIDS@Home
Thread: Experiment 37 coming to an end - what's next ? VINA version ? |
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Thread Status: Active Total posts in this thread: 14
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herflick
Senior Cruncher Joined: Nov 11, 2009 Post Count: 176 Status: Offline Project Badges: 
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It looks that at the current pace Experiment 37 should be done within the next 3 to 4 weeks. This would signal the start of experiment 38.
Does anyone know if Experiment 38 will use AutoDock VINA instead of AutoDock 4 to complete the work units ??? Based on the official VINA website it appears that VINA is much faster than AudtoDock 4. It's also my understanding that some of the other projects on WCG already implemented VINA. Either way, I'm happy that we are all making progress with our WU  Discussion of VINA on FAAH has been talked about several months ago in previous post . |
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martin64
Senior Cruncher Germany Joined: May 11, 2009 Post Count: 445 Status: Offline Project Badges: 
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Dr. Perryman previously announced that Experiment 38 would even be a larger one than #37. He didn't mention any departure from the current settings. But they will gain experience with Vina in their new project, which could lead to changes in FAAH as well. Just speculation.
---------------------------------------- Regards, Martin  |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Dr. Perryman also explained in the GFAM introduction, that different results are produced between AutoDock and Vina and for first time at WCG, a science, GFAM, will be processed by both. I'm sure he'll be using this as a benchmark to see which dockings are matching and which produces the best hits and which of the engines missed any important finds.
In short, plans are always subject to change, but it's save to share that 2011 wont see any alteration to the FAAH engine used i.e. if #38 is imminent, it will be on the known AutoDock version. --//-- |
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mgl_ALPerryman
FightAIDS@Home, GO Fight Against Malaria and OpenZika Scientist USA Joined: Aug 25, 2007 Post Count: 283 Status: Offline Project Badges:
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Hello herflick,
The jobs for Experiment 38 have already been created and tested, and many of them have already been submitted to the IBM team at World Community Grid. I just haven't updated the Status page with a description of this experiment yet. I'll try to do that update fairly soon. Experiment 38 uses AutoDock to search for new allosteric inhibitors of HIV integrase. This experiment is in fact a biiiiiiiiiiig one! It involves several thousand different batches. It will at least run through batch # 29155, and I will probably extend it a bit farther than that, too. I've started planning Experiment 39, as well, but I haven't started creating the inputs for it yet. Exp. 39 will also use AutoDock. For the near future, we'll just use AutoDock on FightAIDS@Home, and we'll test some of the top-ranked compounds locally (at TSRI) using Vina, like we did with the top compounds from Experiment 28 (see Volume 10 of the FightAIDS@Home Newsletter at http://fightaidsathome.scripps.edu ). But at some point in the future, we do plan to use both AutoDock and Vina to screen compounds on FightAIDS@Home. Thank you for your interest and your support, Dr. Alex Perryman |
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Rickjb
Veteran Cruncher Australia Joined: Sep 17, 2006 Post Count: 666 Status: Offline Project Badges: 
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Thanks for your information on "ordinary" AutoDock as used by FAAH vs VINA, Dr P.
If the results from the 2 versions are different, then are the results from one "more valid" than results from the other? Are the results similar, eg the set of best ligands for one overlaps with the set from the other? Would a significant number of interesting ligands be missed by screening with one and not the other? While on the subject of VINA, will it be possible to make projects that use it single-redundancy? Then there is the experience of the DDDT team, who found that AutoDock produced many false positives when docking against their flaviviridae protease models, so they switched to screening with CHARMM for DDDT2. Are their findings relevant to other AutoDock/VINA projects, including FAAH? |
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Falconet
Master Cruncher Portugal Joined: Mar 9, 2009 Post Count: 3295 Status: Offline Project Badges: 
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Regarding the DDDT experience read this
----------------------------------------https://secure.worldcommunitygrid.org/forums/...ad,31228_offset,10#324654 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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Rickjb
Veteran Cruncher Australia Joined: Sep 17, 2006 Post Count: 666 Status: Offline Project Badges:
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Thanks, Falconet - I'd missed that thread. (it would be good to be able to collect all the bits of tech wisdom from the WCG projects' scientists in one easy-to-find place, but I don't know how to do it).
I find Al Perryman's paragraph about using both AutoDock Standard and VINA of particular interest: "The idea of using a different docking program to perform a second round of testing is a great idea. In fact, I recently used a protocol like that to identify two active fragments from the results of FAAH Experiment 28. First, I used the AutoDock results from FightAIDS@Home to identify a couple hundred promising compounds. I then re-docked those compounds on our cluster at TSRI to confirm the results from World Community Grid. I then docked all of the top compounds again using the new docking program "AutoDock VINA," which uses a different search algorithm and a different scoring function. Out of the compounds that scored very well with both AutoDock and VINA, 10 fragments were purchased and assayed by our collaborators. In the preliminary results, 2 of these 10 compounds were shown to inhibit HIV protease. These two active fragments are still being tested in additional assays, but I should be able to start writing a paper on these results soon." It doesn't answer the questions "which docking program is best?", or "are there useful compunds that score well on 1 or the other but not both docking progams?". I guess someone would have to spend more time and $$ doing the experiments with real chemicals to answer those. Stuff for the inevitable "suggested further research" basket. And it doesn't answer the question re DDDT2's switch to screening with CHARMM. Or whether single-redundancy is possible for VINA projects, and if so, whether there is any progress in implementing it. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Rickj
----------------------------------------One way to be able to collect all the bits of tech wisdom from the WCG projects' scientists is to look at WCG Index , they post in every thread when they can hope this help , if not reply to me and with pleasure can try to find for another way [Edit 2 times, last edit by Former Member at Nov 21, 2011 3:31:54 PM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
To precise what JP says:
----------------------------------------Forum Posts by Project Primary Investigators & Scientists Rev Nov 6, 2010 Since Dr. Perryman also does GFAM, it saved me the time to add this science to the table... I've just extended the project header :D. If I missed any posting project scientist's name in the table, just drop a note in Website support. --//-- edit: Yes I did miss to add the scientist, replacing Malmstrom [Edit 1 times, last edit by Former Member at Nov 21, 2011 3:43:46 PM] |
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herflick
Senior Cruncher Joined: Nov 11, 2009 Post Count: 176 Status: Offline Project Badges:
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It looks like Project 38 work-units will start being sent out today.
The lastest project 37 WU I got was from batch 26,162 and project 38 should be starting out at batch 26,179. We are only 17 batches away !  |
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