I don't know...

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I don't know...

Postby Jordan Joestar » Thu Jul 04, 2013 3:26 pm

Hi!
My name is Jordan and I am a student of chemistry from Italy. Tuesday I have an exam of Biopolymers and I have to use PyRx for docking. My prof. gave me a human protein and I choice the cortisol as a ligand. I did docking and now I have 9 different results.
My prof said me that after the docking I must write a small report in which I have to describe all the types of interaction of ligand with the human protein. Unfortunately my prof didn't say how can we know all the interactions: hydrogen bond, Van Der Waals forces, aromatic interactions, etc.
Someone could help me? PyRx could show me all the types of interactions? If no, which other program could help me?

Thanks. :)
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Re: I don't know...

Postby sargis » Fri Jul 05, 2013 8:00 pm

Hi Jordan,

Thanks for the message. Glad to see you were able to use and get results with PyRx. I have implemented hydrogen bond visualization for 0.9 version of PyRx (https://sourceforge.net/apps/trac/pyrx/roadmap). I haven 't had a chance to implement Van Der Waals forces, aromatic interactions, etc. visualization in PyRx. You can try ADT or other software to visualize and describe these types of interactions.

Perhaps someone else can provide input on which other program could help you.

Best,
Sargis
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Re: I don't know...

Postby Jordan Joestar » Sat Jul 06, 2013 5:50 pm

sargis wrote:Hi Jordan,

Thanks for the message. Glad to see you were able to use and get results with PyRx. I have implemented hydrogen bond visualization for 0.9 version of PyRx (https://sourceforge.net/apps/trac/pyrx/roadmap). I haven 't had a chance to implement Van Der Waals forces, aromatic interactions, etc. visualization in PyRx. You can try ADT or other software to visualize and describe these types of interactions.

Perhaps someone else can provide input on which other program could help you.

Best,
Sargis


Thank you very much for the answer. :)
I've downloaded the file "PyRx 0.9" but I don't know how to install it. I tried to put the files on "C:\Program Files\PyRx\Lib\site-packages" but when I open PyRx the symbol "H" for show the hydrogen bonds don't appear.
I tried to use AutoDock Tools but our prof didn't teach us how to use this program.

Could you tell me how can I see the Van Der Waals forces and aromatic interactions with AutoDock Tools?

Tuesday I have the exam and my friends told me that they don't know how to see these interactions, so, they'll try to invent a plausible explanation.
Isn't possible do an exam in this conditions. We want know how to use this program but our teacher is incompetent... excuse me if I'm angry but that's a shame. :evil:
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