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Hi,

You could try CASTp (http://sts.bioengr.uic.edu/castp/). If your protein is in the pdb it may well be in their database, if not, just upload it.

  Cheers,

            Boaz

 
 
Boaz Shaanan, Ph.D.                                        
Dept. of Life Sciences                                     
Ben-Gurion University of the Negev                         
Beer-Sheva 84105                                           
Israel                                                     
                                                           
E-mail: [log in to unmask]
Phone: 972-8-647-2220  Skype: boaz.shaanan                 
Fax:   972-8-647-2992 or 972-8-646-1710    
 
 
                


From: CCP4 bulletin board [[log in to unmask]] on behalf of Zhou, Tongqing (NIH/VRC) [E] [[log in to unmask]]
Sent: Thursday, May 31, 2012 8:41 PM
To: [log in to unmask]
Subject: [ccp4bb] Calculation of volume/size of cavity

Dear All,

 

I am looking for a way to calculate the size of a protein cavity which is occupied by a loop from a ligand protein. The goal is to see what’s the maximum length of peptide allowed in this cavity.

 

Thanks,

 

Tongqing

 

Tongqing Zhou, Ph.D.

Staff Scientist

Structural Biology Section

Vaccine Research Center, NIAID/NIH

Building 40, Room 4609B

40 Convent Drive, MSC3027

Bethesda, MD 20892

(301) 594-8710 (Tel)

(301) 793-0794 (Cell)

(301) 480-2658 (Fax)

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