ADL: how do you select the right protein ?

Rupal Chauhan chauhanrupal757 at gmail.com
Fri May 25 05:22:49 PDT 2012


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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