ADL: Flexible residues, Vol 87, Issue 13

Dr Muralikrishna Kumar sdis_au at rediffmail.com
Tue Nov 15 20:20:56 PST 2011


 
  
  HiThere are certain rules given in the following publications for fixing flexible residues in a receptor pocket. Hope it helps you.Anderson A. C., O’Neil R. H., Surti T. S. and Stroud R. M.,
  Chem. Biol., 8,
  445 (2001).
  
 
 
  
  Sherman
  W., Day T., Jacobson M. P., Friesner R. A. and Farid R., J. Med. Chem., 49, 534 (2006).
  
 
 
  
  Rarey M., Kramer B., Lengauer
  T. and Klebe G., J. Mol. Biol.,
  261, 470 (1996).
  
 
Dr.M Murali Krishna Kumar

Assistant Professor,

Pharmaceutical Chemistry Research Labs,

College of Pharmaceutical Sciences,

Andhra University,

Visakhapatnam - 530003



http://sdisau.blogspot.com/

09441419246


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Subject: autodock Digest, Vol 87, Issue 13
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Today's Topics:



   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)





----------------------------------------------------------------------



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

Message-ID:

   <OFAEFD59A8.A34881D6-ON86257948.00796B5F-86257948.00796B5F at us.ibm.com>

Content-Type: text/plain; charset=US-ASCII





I will be out of the office starting  11/14/2011 and will not return until

11/16/2011.



I will respond to your message when I return.



------------------------------



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

Message-ID:

   <CAGSFR4HmDD0NkaaLgJ2-bcoawrYHnKNL5j4G_o8U13vVgkH9sQ at mail.gmail.com>

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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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