ADL: autodock Digest, Vol 93, Issue 16

Julio Dominguez acheron24 at hotmail.com
Mon May 21 18:26:29 PDT 2012


Hi Mohammad, hi Sarah,

To add my two cents I would like to say that there is no single criteria but I read something for doing electrostatic calculations that may be useful here:

"use all of them and make an average"

That sounds silly but what I mean is: if there are a lot of structures in the PDB it is because they are not quite the same. Even taking into account the aspects Sarah mention, there might be subtle differences such as single point mutations, loops in different conformations, different number of solved residues (N-termini and C-termini are sometime too flexible) and NMR-solved structures (these could have many model per PDB entry). So, bottom line is: use them all and while you wait for the dockings to finish read the papers that describe the structures so that you know where the differences are.

Good luck and let us know if you need/want further examples/help.

> 
> --------------------
> 
> Message: 3
> Date: Mon, 21 May 2012 06:49:39 -0700
> From: "sarah k. " <crimsonflower at gmail.com>
> Subject: Re: ADL: how do you select the right protein ?
> To: autodock at scripps.edu
> Message-ID:
> 	<CAMxoDDAayXNYaY=VnJEPWFP4iWO_pAQzGWHZpAJk5B+WN3=K_w at mail.gmail.com>
> Content-Type: text/plain; charset=ISO-8859-1
> 
> 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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> End of autodock Digest, Vol 93, Issue 16
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