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World Community Grid Forums
Category: Completed Research
Forum: FightAIDS@Home
Thread: Seemingly strange alignment |
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Thread Status: Active Total posts in this thread: 20
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
If the image is of the current process is of any indication as to what is happening, then I happen to have a somewhat strange alignment.
Instead of aligning it to the pocket of the molecule it seems to be aligned to an outer part of the chain. Or does it now calculate some conformational change in the target chain to inhibit it's function? I have uploaded a screenshot on rapidshare. faah.gif |
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
It does look a little unusual.
My understanding is that AutoGrid creates coordinates for starting the docking attempts with AutoDock. Possibly it's a bad work unit, possibly it's an unusual work unit, or maybe everything is going normally. Well, that was a lot of help. Perhaps a FAAH scientist can comment? (Note: you may have to wait a while before a scientist manages to reply.) For the convenience of others, I have included your image here:  |
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Sekerob
Ace Cruncher Joined: Jul 24, 2005 Post Count: 20043 Status: Offline |
looked at one on BOINC, just starting a new attempt at 58% (green line in best energy at beginning, red dotted line going the full width of the graph).... virtually the same image as on the above WU.... I'll have a watch if it moves anywhere towards the end of the attempt.
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WCG
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Ok I am going to have look later on maybe it still changes. Thanks anyway for the reply.
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
All of mine on all of my machines have looked like this recently too - all on the outside.
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Diana G.
Master Cruncher Joined: Apr 6, 2005 Post Count: 3003 Status: Offline Project Badges: 
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I have had this same thing going on for a while. I just was waiting to see if anybody else brought it up. I told Robby about it a couple weeks ago, but since all my WU's are valid I just let it go.
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
Just throwing out some suggestions:
This could be another experiment, checking how molecules that have been found to bind strongly in the active site behave when the entire protease structure is taken into account. For example, the drug may not be so effective if the molecule binds preferentially to a different part of the protease. Or this could be the end of an experiment, where the scientists are throwing in some less likely candidates, or they are trying again using different parameters on candidates that failed on a previous attempt. WCG do tend to defer troublesome work unit batches to the end of projects. Speculation is fun! |
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Diana G.
Master Cruncher Joined: Apr 6, 2005 Post Count: 3003 Status: Offline Project Badges:
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Thanks Didactylos! Fun it is!! I really enjoy seeing it outside and have wondered these same things. Good to know I am not abby-normal in my speculations LOLOLOL
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Former Member
Cruncher Joined: May 22, 2018 Post Count: 0 Status: Offline |
If the image is of the current process is of any indication as to what is happening, then I happen to have a somewhat strange alignment. Instead of aligning it to the pocket of the molecule it seems to be aligned to an outer part of the chain. Yes, the image is an indication of what is happening and, yes, it's different than what you're accustomed to. The difference is intentional and I'm delighted that you noticed! As your images shows, one of the docking experiments we are currently running on the World Community Grid is designed to identify molecules that might bind specifically to the "outer part" of the protease. We call this "outer part" the "exo-site" and distinguish it from the "active site" in the central part of the protease where current protease drugs are known to bind. The basis for this experiment (docking to the exo-site) is described in this paper (Protein Sci. 2004 Apr;13(4):1108-23 ) by colleagues of ours across the street at the University of California, San Diego. Here in the Olson lab, we have independent modeling results which also suggest this "exo-site" is of interest. It was that combination (the modeling results from UCSD and from our lab) that piqued our curiosity and motivated the experiment you see running at the moment. Thanks for noticing and, of course, thank you very much for your participation! Lindy |
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Sekerob
Ace Cruncher Joined: Jul 24, 2005 Post Count: 20043 Status: Offline |
Hi Lindy,
----------------------------------------While your at it and the observations of 'this experiment', your progress website has been indicating 50% progress on experiment 5 and experiment 6 in preparation for about 5-6 months now. Are we talking this to be part of 5 or is this 6? With Autodock 4 Update being readied for launch, does that imply 6 is in fact running to an end? hungry for 'progress' info.
WCG
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