ADL: how do you select the right protein ?

Rupal Chauhan chauhanrupal757 at gmail.com
Sat May 26 20:36:08 PDT 2012


ok. Thank you  Sarah.

-Ruapl Chauhan

On Sat, May 26, 2012 at 3:01 PM, sarah k. <crimsonflower at gmail.com> wrote:

> Dear Rupal,
>
> Usually, interactions with a binding constant of 10^(6 to 10) are
> considered to be strong. the binding energy (or dG) equals -nRlnK or
> dG= -N(KB)lnK. boltzman cte is about 10^(-23) so your binding cte
> exhibits a good binding. You'd better calculate them once to get sure
> about binding cte and check littereture to see tjhe range of K
> acceptable for your work.
>
> Sarah
>
> On 5/25/12, Rupal Chauhan <chauhanrupal757 at gmail.com> wrote:
> > Hello,
> >
> > I'm using AutoDock for the first time, and I am just wondering if a
> > binding energy of -2.49 is good or bad? this was the best result (1_1)
> > generated, with the lowest binding energy.
> >
> > Any help would be greatly appreciated.
> >
> > -Ruapl Chauhan
> >
> > On 5/21/12, sarah k. <crimsonflower at gmail.com> wrote:
> >> Dear Mohammad,
> >>
> >> First, you should consider the exact functionality of your protein.
> >> You should choose whether your protein should refer to Homo sapiens or
> >> any other host.
> >>
> >> Most pdb files consist of proteins complexed with special ligands or
> >> inhibitor and several ions. Based on the microenvironment of your case
> >> protein, chosing one of them can be superior. For example, if your
> >> seraching an calcium channel protein, a structure with Ca cations MAY
> >> work for you better.
> >>
> >> If none of the conditions above helped, you should choose the pdb file
> >> with the highest! resolution. If you want your pdb file represent the
> >> exact conformation of the protein in cell, you should perform
> >> Molecular dynamics simulation.
> >>
> >> Best regards,
> >> Sarah
> >>
> >> On 5/21/12, Mohammad Goodarzi <mohammad.godarzi at gmail.com> wrote:
> >>> Dear,
> >>>
> >>> I have a question, How do you select the right protein for docking
> >>> studies?
> >>> For example, let's say HIV-1, if you search this in PDB, you will have
> >>> many
> >>> proteins.
> >>> Ok, the first step is to see what is the resolution and the one with
> >>> lowest
> >>> resolution is preferred.
> >>> but what more?
> >>>
> >>> I am looking forward to hearing from you.
> >>> Sincerely Yours,
> >>> Mohammad
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> >
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