ADL: how do you select the right protein ?

sarah k. crimsonflower at gmail.com
Sat May 26 02:31:30 PDT 2012


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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