ADL: Question about molecular docking on glycoproteins

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ADL: Question about molecular docking on glycoproteins

Jonathan Y Wang
I was doing some molecular docking and I ran across a question I was hoping
you could help me with some insight on.
Most docking is with enzymes but I'm observing a glycoprotein right now and
having difficulty with the binding frames. It seems that the ligands always
seem to want to bind to the outside of the structure (undoubtedly where
another monomer will tessellate to form a viral capsid). How do I go about
removing that?
Additionally, I tried prepping my receptor for molecular docking by
removing the waters and it caused the binding frames to bind totally
different and end up with zero polar contacts. To me this seems a bit fishy
considering it bound correctly when the molecule was not "prepped". Can I
assume that these waters then are pretty essential to the integrity of the
receptor? None of the papers I'm reading seem to mention water molecules so
I didn't know if it was just understood or if they did something different.
Like they say, science is never black and white, haha.

--
Biology and Radio-Television-Film double major
University of Texas at Austin 2018
Research Intern Taipei Medical University
Dr. Lin Liang-Tzung
Cinematographer: CTB Productions
Pronouns: He/Him They/Them
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Re: ADL: Question about molecular docking on glycoproteins

Leandro Bortot
     It seems like you are making blind docking, i.e. docking in which the
search volume comprises the whole protein.
     You can remove the dimerization interface from your search volume if
you want it to exclude it from the docking. Alternatively, you can use the
oligomer in the docking.


     Waters are sometimes important for binding. But in this case it seems
there is a problem with protein/ligand preparation

Best regards,
Leandro

On Sun, Sep 17, 2017 at 2:24 PM, Jonathan Y Wang <
[hidden email]> wrote:

> I was doing some molecular docking and I ran across a question I was hoping
> you could help me with some insight on.
> Most docking is with enzymes but I'm observing a glycoprotein right now and
> having difficulty with the binding frames. It seems that the ligands always
> seem to want to bind to the outside of the structure (undoubtedly where
> another monomer will tessellate to form a viral capsid). How do I go about
> removing that?
> Additionally, I tried prepping my receptor for molecular docking by
> removing the waters and it caused the binding frames to bind totally
> different and end up with zero polar contacts. To me this seems a bit fishy
> considering it bound correctly when the molecule was not "prepped". Can I
> assume that these waters then are pretty essential to the integrity of the
> receptor? None of the papers I'm reading seem to mention water molecules so
> I didn't know if it was just understood or if they did something different.
> Like they say, science is never black and white, haha.
>
> --
> Biology and Radio-Television-Film double major
> University of Texas at Austin 2018
> Research Intern Taipei Medical University
> Dr. Lin Liang-Tzung
> Cinematographer: CTB Productions
> Pronouns: He/Him They/Them
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---