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Re: [ccp4bb]: How big is my active site?
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Dear Jim,
Perhaps the CAST server could help you:
http://cast.engr.uic.edu/cast/
Salam
>
>Does anyone know of a good way to look at the volume of an active site? This
>begs the question of how one defines the extent of an active site of course.
>We have a two related proteins with beta sandwich into which substrates are
>bound. One site looks bigger on the screen than the other. In this case size
>may matter. Does anyone have a good idea how I could go about quantifying
>that? Voidoo does not recognise it as a cavity (it is not of course a
>cavity, more a large dent). If I could understand the CCP4 program volume
>documentation that may help but I can't. Any other approaches?
>
>thanks
>Jim
>
>
>James H. Naismith | Research mailto:naismith@st-and.ac.uk
>Professor of Chemical Biology | Teaching mailto:jhn@st-and.ac.uk
>BBSRC Career Development Fellow |
>Centre for Biomolecular Sciences | Office: 1334-463792 (24 hr)
>The North Haugh | Fax : 1334-467229
>The University | Lab : 1334-467245
>St. Andrews | In UK add 0 to start of number
>Fife Scotland, U.K., KY16 9ST | www http://speedy.st-and.ac.uk/
>
>
>
--------
Salam Al-Karadaghi, Assoc. Prof.
Molecular Biophysics,
Chemical Centre,
Lund University
Getingev. 60
PO Box 124, 221 00 Lund,
Sweden
Tel. Int+46 (0)462224512
Fax. Int+46 (0)462224692
Web: http://www.mbfys.lu.se
--------