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Thread Status: Active Total posts in this thread: 53
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Sekerob
Ace Cruncher Joined: Jul 24, 2005 Post Count: 20043 Status: Offline |
Looked thru the checkpoint log entries and count about 32 attempts per job. I think we need the techs or watowich to tell us how much is packed. WCG nor a scientist would engage in an open ended project, thus for now either the 1 year calendar or 50,000 CPU years does feel like a realer number. That said, the estimates have been off pretty much all the time (speak running considerable longer). Look at the HCMD story e.g.
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WCG
----------------------------------------Please help to make the Forums an enjoyable experience for All! [Edit 2 times, last edit by Sekerob at Aug 24, 2007 2:46:41 PM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Watowich estimates the analysis will require comparing about 6.5 million molecules to 50 different variants of the protein. most of the time we do blind docking.. We scan all compounds from the data bases like zinc/pubchem(which are approx 6millions). If you think about zinc database itself then you will find many entries are repeated(same structures, they are also mentioned by ids in zinc database itself) so removing them before starting docking will save half of the time. Next, sometime docking experiments are done with out knowledge of active site! specially if we don't know the grid center. This again waste lot of CPU time. Yesterday, I was checking the average CPU time and it is about approx 8 hours per compound which is 6 times more than running autodock locally. If we want to save CPU time and speed up the docking process then def we have to some pharmacaphore analysis, screen list of zinc database compund before sending them to docking experiment. This will reduce the number of compound by 1/10th and also help us to analyze the docked compound/structures in record time. Just a suggestion. |
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JmBoullier
Former Community Advisor Normandy - France Joined: Jan 26, 2007 Post Count: 3716 Status: Offline Project Badges:
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Thanks for coming to rescue me esoteric17.
---------------------------------------- I have no doubt that watowich is not trying to confuse us but there are obviously some parameters that we are missing, and that is what I asked for. Regarding the 50,000 CPU years figure I would not give it much importance when trying to find how long it will take us to complete this project (in real human calendar months): I consider that such preliminary figures can be used only for guessing if the project is small, big or huge, nothing more precise. And, of course, I would not try to extrapolate the current "ramping-up" daily figures either: most people don't know yet that there is a new project that they can select. And only if/when they have migrated to Boinc. Not forgetting either the Boinc agents which run with many days of queued WUs and are only just about to start DDDt eventually. Thank you too, ssnegi, for explaining how it may be possible to reduce the raw theoretical number of cases to a more realistic number of real WUs. Cheers. Jean. |
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twilyth
Master Cruncher US Joined: Mar 30, 2007 Post Count: 2130 Status: Offline Project Badges:
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We scan all compounds from the data bases like zinc/pubchem(which are approx 6millions). For the convenience of readers - I had never heard of the Zinc database: ZINC, a free database of commercially-available compounds for virtual screening. ZINC contains over 4.6 million compounds in ready-to-dock, 3D formats. See Zinc If we want to save CPU time and speed up the docking process then def we have to some pharmacaphore analysis, screen list of zinc database compund before sending them to docking experiment. Also never heard of pharmacaphore The pharmacaphore is the structural fragment/part of molecule which: makes it of use as a drug. or has the right/desired effect (on the body) or fits/binds to receptor/active site or is pharmacologically active or is common to all drugs of that type See Chemistry - page 13 Is Zinc the database used for DDDT and/or other projects? Are any other databases used? ![]() ![]() |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Is Zinc the database used for DDDT and/or other projects? We've also used (part of? "fragment"?) ZINC for FAAH: http://fightaidsathome.scripps.edu/ Experiment 7a2: 93% Completed: x2BPW vs ZINC Fragment Library (exo site) Experiment 7b1: 93% Completed: x2AZ8 vs ZINC Fragment Library (active site) Experiment 7b2: 93% Completed: x2AZ8 vs ZINC Fragment Library (exo site) |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
I think we need the techs or watowich to tell us how much is packed. Just bumping this thread for some further information from WCG and/or watowich regarding how many ligands are per WU (or correction of the past estimate of 6.5m ligands) ![]() [Edit 1 times, last edit by Former Member at Aug 28, 2007 5:14:21 PM] |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
agree.
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
OK! Maybe I come back.
Whats the average time between checkpoints? I dropped out when the Help Cure Muscular Dystrophy project went into hibernation. Those checkpoints averaged about 30 min. to 1 Hr on my computer. FAAH & HPF are unworkable for me. I run a 1.73 Ghz Athalon XP processor at 70% and reboot my PC 3 to 5 times a day. (No. I do not use the hibernate function.) I am, using BOINC, and run my PC about 60 to 70 hrs a week. Jack |
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JmBoullier
Former Community Advisor Normandy - France Joined: Jan 26, 2007 Post Count: 3716 Status: Offline Project Badges:
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Whats the average time between checkpoints? Between 15 and 20 mn most of the time for me (P4 2.4 GHz). With a few WUs between 15 and 10 mn. Cheers. Jean. |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
(Checkpoints are) Between 15 and 20 mn most of the time for me (P4 2.4 GHz). With a few WUs between 15 and 10 mn. Cheers. Jean. Sounds great! Thanks Jack |
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