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AutoDock, AutoLigand, MGLTools, Vina, PyRx and more.
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PostPosted: Sat Dec 28, 2013 3:19 am 
Millimolar User
Millimolar User
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Joined: Sat Dec 28, 2013 2:58 am
Posts: 1

I'm a begginer in this field so I have some questions and I want to confirm my strategy.

My interest is to study metabolite docking and screening of enzyme inhibitors.

These are my questions.

First question : I'm trying to dock metabolite and ligand library into a enzyme. vina is suitable for this work?

If possible,
Second question : In the absence of cofactor in enzyme pdf file, How can I deal with cofactor?

Third question : My final goal is to search enzyme inhibitors,

these are my plans

1. Download enzyme PDB file
2. Energy minimization of enzyme structure using chimera or Rosetta
3. Predict ligand binding site using autoligand
3. Prepare ligand library using raccoon
4. Docking ligand to enzyme by using vina
5. Analyzing results
6. (optional) MD simulation

I’d happy to take any comments.

Thank you

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