questions about running autodockvina in pyrx

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questions about running autodockvina in pyrx

Postby mai el-naggar » Tue Nov 05, 2013 12:53 am

Hi,
I am doing docking using autodock vina in pyrx 0.8, I have some questions.
-Is it necessary to prepare the receptor using ADT? or it is enough to prepare it using pyrx by copying hetero-atom residues corresponding to the co-crystallized ligand into a new file and removing all hetero-atom residues from the protein crystal structure file except that for Zn as it enter in the interaction between the ligands and my receptor.
-when using open Babel, is it important to change the preferences of open babel autodock ligand partial charge into open Babel instead of byBapel, what is the importance of this step.
- Is it possible to change the docking algorithm and the docking parameters using this version of pyrx.
- Why in analyzing results the internal, torsional, and unbond energy don't appear? only binding affinity, mode, RMSD lower and upper bound appear.
-I know that the lowest binding affinity and the closest to the co-crystallized ligand is the best, but do I judge the docking results only from the binding affinity, how can RMSD values affect the docking results?
-different modes of the docked ligand have different binding energies, do I choose the binding energy of the mode that is mostly superimposed with the co-crystallized ligand? or I just use the lowest binding energy.
- how can I make visualization of the ligand-receptor interaction using ICM browser?
thanks in advance, and best regards
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Re: questions about running autodockvina in pyrx

Postby sargis » Tue Nov 05, 2013 6:52 pm

Hi,

Good questions. I'll try to answer them below.

mai el-naggar wrote:-Is it necessary to prepare the receptor using ADT? or it is enough to prepare it using pyrx by copying hetero-atom residues corresponding to the co-crystallized ligand into a new file and removing all hetero-atom residues from the protein crystal structure file except that for Zn as it enter in the interaction between the ligands and my receptor.

It is not necessary to prepare the receptor using ADT, it is enough to prepare it using pyrx. pyrx version 0.9 handles hetero-atom residues better, but you can use pyrx 0.8 and edit the protein crystal structure file as you described above.

mai el-naggar wrote:-when using open Babel, is it important to change the preferences of open babel autodock ligand partial charge into open Babel instead of byBapel, what is the importance of this step.

It is not important to change the preferences of open babel autodock ligand partial charge into open Babel instead of PyBabel. I did some experiments with partial charges and found that this default leads to better results as described in the following blog post:Open Babel Partial Charges. I implemented the option for choosing partial charges for doing this kind of experiments. This option is not important unless someone else wants to do similar experiments.

mai el-naggar wrote:- Is it possible to change the docking algorithm and the docking parameters using this version of pyrx.

It is possible to change the docking parameter, but this feature is not well tested. Regarding changes to the docking algorithm, what kind of docking algorithm you have in mind?
mai el-naggar wrote:- Why in analyzing results the internal, torsional, and unbond energy don't appear? only binding affinity, mode, RMSD lower and upper bound appear.

Analyze Results page for Vina and AutDock wizard have different columns, since these two programmes output different results. AutDock 4 outputs the internal, torsional, and unbond energy, while Vina outputs binding affinity, mode, RMSD lower and upper bound.

mai el-naggar wrote:-I know that the lowest binding affinity and the closest to the co-crystallized ligand is the best, but do I judge the docking results only from the binding affinity, how can RMSD values affect the docking results?
-different modes of the docked ligand have different binding energies, do I choose the binding energy of the mode that is mostly superimposed with the co-crystallized ligand? or I just use the lowest binding energy.
- how can I make visualization of the ligand-receptor interaction using ICM browser?
thanks in advance, and best regards

Sorry, I wont have time to answer these questions, but you are welcome to use Support this project link at http://pyrx.sourceforge.net/ to tip (i.e. voluntary additional payment made for services rendered) me for these answers.
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Re: questions about running autodockvina in pyrx

Postby mai el-naggar » Sun Nov 10, 2013 10:11 am

Thank you so much sargis for your answers
Good Luck
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