ADL: comparision of different ligands.

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ADL: comparision of different ligands.

neelam wafa
Hello all
I have docked a number of ligands using vina. i want to compare these with
the reference ligand.  how can find that given ligand is hiw many times
more effiective than refrence by comparing the  free energy value. is there
any specific formula?  if my refrence is giving -9.1 value and ligand
-11.5. then how many times it is beter than refrence?
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Re: ADL: comparision of different ligands.

Leandro Bortot
You can check "binding constant" in wikipedia to see the formulas =)

Please keep in mind that these numbers you mention come from the scoring
function.
If you want to use then as predictors of the actual free energy you should
consider the expected error, which is around 2.7 kcal/mol in Vina according
to the original publication.

Best regards,
Leandro


On Mon, Sep 18, 2017 at 2:33 AM, neelam wafa <[hidden email]> wrote:

> Hello all
> I have docked a number of ligands using vina. i want to compare these with
> the reference ligand.  how can find that given ligand is hiw many times
> more effiective than refrence by comparing the  free energy value. is there
> any specific formula?  if my refrence is giving -9.1 value and ligand
> -11.5. then how many times it is beter than refrence?
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
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Re: ADL: comparision of different ligands.

neelam wafa
if i have docked the refrence also with vina, then the error is equal in
both the refrence and ligand and dont need much consideration.  is this.
assumption right or wrong?

On Monday, September 18, 2017, Leandro Bortot <[hidden email]> wrote:

> You can check "binding constant" in wikipedia to see the formulas =)
>
> Please keep in mind that these numbers you mention come from the scoring
> function.
> If you want to use then as predictors of the actual free energy you should
> consider the expected error, which is around 2.7 kcal/mol in Vina according
> to the original publication.
>
> Best regards,
> Leandro
>
>
> On Mon, Sep 18, 2017 at 2:33 AM, neelam wafa <[hidden email]
> <javascript:;>> wrote:
>
> > Hello all
> > I have docked a number of ligands using vina. i want to compare these
> with
> > the reference ligand.  how can find that given ligand is hiw many times
> > more effiective than refrence by comparing the  free energy value. is
> there
> > any specific formula?  if my refrence is giving -9.1 value and ligand
> > -11.5. then how many times it is beter than refrence?
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
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Re: ADL: comparision of different ligands.

Diogo Martins
Hi Neelam,

That's an incorrect assumption - the error can be in any direction and be
large or small. For example, you can have an error of +2 for one molecule,
and an error of -3 for another molecule.

On 18 September 2017 at 10:42, neelam wafa <[hidden email]> wrote:

> if i have docked the refrence also with vina, then the error is equal in
> both the refrence and ligand and dont need much consideration.  is this.
> assumption right or wrong?
>
> On Monday, September 18, 2017, Leandro Bortot <[hidden email]>
> wrote:
>
> > You can check "binding constant" in wikipedia to see the formulas =)
> >
> > Please keep in mind that these numbers you mention come from the scoring
> > function.
> > If you want to use then as predictors of the actual free energy you
> should
> > consider the expected error, which is around 2.7 kcal/mol in Vina
> according
> > to the original publication.
> >
> > Best regards,
> > Leandro
> >
> >
> > On Mon, Sep 18, 2017 at 2:33 AM, neelam wafa <[hidden email]
> > <javascript:;>> wrote:
> >
> > > Hello all
> > > I have docked a number of ligands using vina. i want to compare these
> > with
> > > the reference ligand.  how can find that given ligand is hiw many times
> > > more effiective than refrence by comparing the  free energy value. is
> > there
> > > any specific formula?  if my refrence is giving -9.1 value and ligand
> > > -11.5. then how many times it is beter than refrence?
> > > ________________________________________________
> > > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list
> ---
> > >
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> >
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
________________________________________________
--- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
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Re: ADL: comparision of different ligands.

Mr. Pramodkumar P Gupta
In reply to this post by neelam wafa
Dear Researcher,
In case of molecular interaction study, don't depend only on the docking or
binding energy, though the least energy complex is stable one, consider
pharmacophoric interactions too.....

Regards,

On Monday, September 18, 2017, neelam wafa <[hidden email]> wrote:

> Hello all
> I have docked a number of ligands using vina. i want to compare these with
> the reference ligand.  how can find that given ligand is hiw many times
> more effiective than refrence by comparing the  free energy value. is there
> any specific formula?  if my refrence is giving -9.1 value and ligand
> -11.5. then how many times it is beter than refrence?
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>


--
Pramodkumar P. Gupta
Assistant Professor
School of Biotechnology and Bioinformatics
D Y Patil University
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