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How to find the amino acids interaction with ligand?
http://mgl.scripps.edu/forum/viewtopic.php?f=9&t=2521
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Author:  Avanthika [ Wed Dec 04, 2013 9:31 am ]
Post subject:  How to find the amino acids interaction with ligand?

In Autodock 4 result, how do I visualize the interactions between amino acids of a enzyme and the ligand?

I use chimera and Pymol. I read that the quadinates from the resultant dock file should be used. That procedure did not work for me. Please let me know how i can find the interactions between ligand and receptor.

Author:  Ruth Huey [ Mon Dec 09, 2013 10:13 pm ]
Post subject:  Re: How to find the amino acids interaction with ligand?

You could examine the interactions between the receptor and the docked ligand in AutoDockTools:

Part 1 Setup:
Analyze->Dockings->Open
-in the 'Docking Log File' widget which opens select your docking log file + click Open

Analyze->Macromolecule->Open
(this will load your receptor.pdbqt)

Analyze->Clustering->Show
-Click on the lowest energy bar to put the ligand in the best docked pose in this dlg file.

Part 2 Analyze Visualized Interactions:
Analyze->Dockings->Show Interactions
Now ADT shows:
--hydrogen bonds between the ligand + receptor (green spheres)
--close-contacts between atoms ligand and specific atoms in receptor (wire-frame spheres, colored by atom type for the receptor atoms (receptor residues are labelled); patches of color on the molecular surface of the ligand)
--opens the "Binding Site Interactions display options" widget.

This widget can be used to adjust the displayed features AND to output various lists of contacts. These include ligand contacts, receptor contacts' and hydrogen bonds. Clicking on one of these in the drop-down menu results in printing the corresponding list in the python shell of ADT (which is opened by clicking on the button with >>> in a white-box).
eg
ligand contacts:
'residues in 'ligand'-> 'receptor' residues in close contact
1 I:IND201-> B:ASP25, A:ASP25, B:ARG8, B:VAL32, B:VAL82, B:ASP30, B:PRO81, A:ARG8, B:GLY27, B:ILE84, A:LEU23, B:ALA28, B:ASP29, A:VAL82,

receptor contacts:
'residues in 'receptor'-> 'ligand' residues in close contact
1 B:ASP25-> I:IND201,
2 A:ASP25-> I:IND201,
3 B:ARG8-> I:IND201,
4 B:VAL32-> I:IND201,
5 B:VAL82-> I:IND201,
6 B:ASP30-> I:IND201,
7 B:PRO81-> I:IND201,
8 A:ARG8-> I:IND201,
9 B:GLY27-> I:IND201,
10 B:ILE84-> I:IND201,
11 A:LEU23-> I:IND201,
12 B:ALA28-> I:IND201,
13 B:ASP29-> I:IND201,
14 A:VAL82-> I:IND201

hydrogen bonds:
'hydrogen bonds (donor residue->acceptor residue(s))
1 ind:I:IND201-> hsg1:B:GLY27, hsg1:B:ASP25,
2 hsg1:B:ASP29-> ind:I:IND201,
3 hsg1:B:ARG8-> ind:I:IND201'

Author:  Avanthika [ Tue Dec 10, 2013 4:04 am ]
Post subject:  Re: How to find the amino acids interaction with ligand?

Thank you so much.

Works exactly fine. This method is so much better than copying the coordinates of the the best docked ligand and saving it in mol2 format and then using another tool to visualize. :)

Author:  SajanJoseph [ Thu Feb 19, 2015 5:39 am ]
Post subject:  Re: How to find the amino acids interaction with ligand?

I have to write an essay regarding amino acids. Could this help me to complete the essay?

Author:  makably [ Sat Mar 07, 2015 3:24 am ]
Post subject:  Re: How to find the amino acids interaction with ligand?

Avanthika wrote:
Thank you so much.

Works exactly fine. This method is so much better than copying the coordinates of the the best docked ligand and saving it in mol2 format and then using another tool to visualize. :)




Glad To Know Your Query Has Been Solved :)
This Forum Is Really Great :)

Author:  Tanjay [ Mon May 16, 2016 3:27 pm ]
Post subject:  Re: How to find the amino acids interaction with ligand?

Hi everyone,

I have a small problem when it comes to outputting file with contacts list.

I do everything Ruth Huey says in his post but when i do :
Analyze -> Docking -> Write Autodock Virtual Screening Result ligands
It gives me the following error message :

AD41analyze_writeVSResult WARNING
'Analyse - > Macromolecule - > open...' to add ../4xdk.pdbqt to the viewer first

the probelm is that i already did that step and even if i redo it numerous times, it always show this error message to me. How can i output the contacts list i want?

Also, i wanna use this to find the binding between the residues but is there a way to do this without using ADT like using only the dlg file? (no other program needed)

Thanks in advance,

Tanjay

PS : My english isnt too much on point so if anything doesnt sound to clear in my question, i can try and reexplain it better if needed.

Author:  ruggiero [ Sat Feb 18, 2017 4:16 pm ]
Post subject:  Re: How to find the amino acids interaction with ligand?

Hi to all.

I'm using Autodock4.2 for VirtualScreening.
I'm looking for a script that writes in the file "summary_of_results" also the interactions between receptor and the ligand and not only their number such as "summarize_results4.py" does.
Is there a script like this?

Thanks

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