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OfflineChuangTzu
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Molecular Modeling
    #13533909 - 11/24/10 05:55 AM (13 years, 2 months ago)

Just out of curiosity, does anyone here do any sort of modeling of large molecule/complexes or multiple molecule interactions?  Perhaps receptor-ligand modeling, receptor active site modeling, modeling of protein conformations, or something of that nature?


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OfflineSeussA
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Re: Molecular Modeling [Re: ChuangTzu]
    #13534118 - 11/24/10 07:57 AM (13 years, 2 months ago)

I played around with the molecular modeling code used in 'folding@home' for a while, many years ago, but I can't remember the name of it.  I'm sure it is on the site somewhere, as that was where I found it.


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OfflineChuangTzu
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Re: Molecular Modeling [Re: Seuss]
    #13535534 - 11/24/10 01:47 PM (13 years, 2 months ago)

I've been trying to get NAMD running on linux with CUDA support but it's been kind of fruitless so far.  I can still run it without CUDA, but I might not even have nearly enough processing power as it is...

I want to get a basic feel for computing this stuff so I can see how possible some ideas I have are.  If the ideas are feasible and it's only a matter of computing power, it might be worth submitting it to the Shroomery community as an @home project since I believe the ideas are of mutual interest to a lot of people here.


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OfflineSeussA
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Re: Molecular Modeling [Re: ChuangTzu]
    #13535926 - 11/24/10 03:11 PM (13 years, 2 months ago)

Tinker is the package I played around with many years ago.  Amber is another molecular dynamics package used by Folding@home, but I haven't looked at it.  They also use MPI for communication.


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OfflineEllen
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Re: Molecular Modeling [Re: Seuss]
    #13545958 - 11/26/10 10:30 PM (13 years, 2 months ago)

Is there a particular reason? Mostly, I've used UCSF Chimera, or Deepview. If you seriously want to model interactions, it's a huge amount of work. Scripps has Autodock but you have to write for a license.


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OfflineChuangTzu
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Re: Molecular Modeling [Re: Ellen]
    #13546952 - 11/27/10 04:48 AM (13 years, 2 months ago)

For now I just want to learn about what is do-able in terms of current software and hardware capabilities.  I'm well aware that what I actually want to do is a huge amount of work or else it would have been done before.  That, or it is not possible yet for technical reasons.  My purpose right now is to find out which.  If it turns out it is possible, I'll do the legwork getting the software set up and then ask the community here for processing power.  If it's not possible, I'll try to find an alternate way of doing it so that it becomes possible.

Autodock will do part of what I want.  The problem is that the 3D structure of the receptor isn't known.  I will need to calculate it somehow.  Maybe from ab initio folding calculations.  But how accurate are these folding calculations right now?  Do protein structures calculated with, for example, folding@home turn out to be accurate?

If you don't mind my asking, what is your PhD in?

And welcome... : )


Edited by ChuangTzu (11/27/10 11:46 AM)


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Offlineplustax
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Re: Molecular Modeling [Re: ChuangTzu]
    #13551755 - 11/28/10 08:54 AM (13 years, 2 months ago)

I don't see why it's not possible though. You just figure out the encoding region on the genome of cannabis and make a vector and slap that into agrobacterium....


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OfflineChuangTzu
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Re: Molecular Modeling [Re: plustax]
    #13553512 - 11/28/10 04:52 PM (13 years, 2 months ago)

Quote:

plustax said:
I don't see why it's not possible though. You just figure out the encoding region on the genome of cannabis and make a vector and slap that into agrobacterium....




That has little to do with what I want to accomplish actually...


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