ADL: autodock Digest, Vol 87, Issue 13, flexible residues

Lenin Domínguez acheron24 at hotmail.com
Tue Nov 15 12:26:21 PST 2011


Flexibility in the protein world is poorly defined. For autodock it means defined residues that are allowed to change conformation by rotating certain bonds. From the crystallographic point of view, you could assume that B factors reflect flexibility. So if you are using a protein structure derived from XRD check the B factors. 

On Nov 15, 2011, at 12:00, autodock-request at scripps.edu wrote:

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>   1.  Paul Coffman/Rochester/IBM is out of the office. (Paul Coffman)
>   2.  How to know flexible residues in flexible docking (aravind setti)
>   3. Re:  How to know flexible residues in flexible docking
>      (Juan Jose Casal)
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> Message: 1
> Date: Mon, 14 Nov 2011 16:06:13 -0600
> From: Paul Coffman <pkcoff at us.ibm.com>
> Subject: ADL: Paul Coffman/Rochester/IBM is out of the office.
> To: autodock at scripps.edu
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> I will be out of the office starting  11/14/2011 and will not return until
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> I will respond to your message when I return.
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> ------------------------------
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> Message: 2
> Date: Tue, 15 Nov 2011 10:34:28 +0530
> From: aravind setti <aravind.setti at gmail.com>
> Subject: ADL: How to know flexible residues in flexible docking
> To: autodock at scripps.edu
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> I want to do Flexible docking in Autodock
> 
> Is there any way to know the flexible residues of the protein?
> 
> Please help me.
> 
> Thank you
> 
> -- 
> *Regards*
> *Aravind Setti*
> 
> 
> ------------------------------
> 
> Message: 3
> Date: Tue, 15 Nov 2011 09:08:17 -0300
> From: Juan Jose Casal <juan.5ht at gmail.com>
> Subject: Re: ADL: How to know flexible residues in flexible docking
> To: "autodock at scripps.edu" <autodock at scripps.edu>
> Message-ID: <7F24CD29-77A4-4F32-8D42-06E26D7A3E80 at gmail.com>
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> 
> Hi Aravind
> 
> Proteins are not rigids thats why you can set residues flexibilities.
> You can treat them as rigid if you dont want a time of calculation.
> 
> Enviado desde mi iPad
> 
> El 15/11/2011, a las 02:04, aravind setti <aravind.setti at gmail.com> escribi?:
> 
>> I want to do Flexible docking in Autodock
>> 
>> Is there any way to know the flexible residues of the protein?
>> 
>> Please help me.
>> 
>> Thank you
>> 
>> -- 
>> *Regards*
>> *Aravind Setti*
>> ________________________________________________
>> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
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> End of autodock Digest, Vol 87, Issue 13
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