Re: [ccp4bb]: Calculation of protein's cavity

[Jean-Paul Renaud <renaud@titus.u-strasbg.fr>]

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>Dear all,
>
>Are there some powerful tools to calculate the dimension of protein's cavity?
>
>Many thanks for your time,
>
>King Lau
>liaojt@moon.ibp.ac.cn


Try VOIDOO (GJ Kleywegt & TA Jones, Acta Cryst., D50, 178-185 (1994)) at:

http://alpha2.bmc.uu.se/~gerard/usf/voidoo.html.

This program detects cavities and calculates their volume in three ways:
the Van der Waals volume (the complement of the molecular Vanderwaals
surface), the probe-accessible volume (the cavity volume that can be
occupied by the centres of probe atoms), and the probe-occupied volume (the
volume that can be occupied by probe atoms).


Jean-Paul

___________________________________________________________
Dr Jean-Paul RENAUD
Laboratoire de biologie et genomique structurales
CNRS UPR 9004
Institut de Genetique et Biologie Moleculaire et Cellulaire
1 rue Laurent Fries
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F-67404 Illkirch Cedex
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