Hello Yingjie Peng
You can do this in SPOCK. You can select all the residues that make up the
pocket and select calculate, volume from the menu for these residues. Hope
this works.
Arti
> Dear all,
>
> Is there anyone who can tell me how to calculate the volume of
> substrate
> binding pocket in a protein structure? I want to use it to the quantify
> the
> conformational change caused by induced fitting. Thanks very much.
>
> Yingjie Peng
>
> Yingjie PENG, Ph.D. student
> Structural Biology Group
> Shanghai Institute of Biochemistry and Cell Biology (SIBCB)
> Shanghai Institute of Biological Sciences (SIBS)
> Chinese Academy of Sciences (CAS)
> 320 Yue Yang Road, Shanghai 200031
> P. R. China
> 86-21-54921217
> Email: [log in to unmask]
>
Arti S. Pandey
Graduate Student
Chemistry and Biochemistry
Montana State University
Bozeman,MT 59717
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