Dear nathalie,
from the top of my head, I use FLOOD from Upsala software factory: The
program fills in water molecules in the cavity; you can specify a radius
and start from a point in the pdb, like a side chain atom or you can put
a dummy water molecule in the middle of your cavity and start flooding
from there.
I recommend inspecting the flooding result as it might find every little
crack, which might not be what you want, or fill in other unwanted
spaces. This flood pdb can be easily edited in Pymol to remove selected
atoms and get the volume that you want.
To measure this volume, well... I don't remember exactly, but I think
VOIDOO can give you this result. Others might be able to chip in too.
Best of luck.
Vincent
Le 07/07/2020 à 10:21, Nathalie Colloc'h a écrit :
thanks joana,
it is true that you can give a set of coordinates to Caver, but to my
knowledge, Caver look for tunnels only.
It does not seem to compute the volume of surface pockets or internal
cavities.
best
nathalie
Le 06/07/2020 à 15:46, Joana Pereira a écrit :
Hi Nathalie,
I think Caver tools can do that: https://caver.cz/index.php?sid=133
Best wishes
Joana
On 6. Jul 2020, at 15:39, Nathalie Colloc'h <[email protected]
<mailto:[email protected]>> wrote:
Hi everybody,
I am aware of programs which compute the volume of cavities and pockets.
However, I am looking for a program which can compute the volume
around a given point (given by its coordinates), and return also the
information about if it is an open surface pocket or an internal cavity.
Thanks a lot
Nathalie
--
Dr. Nathalie Colloc'h
équipe CERVOxy
ISTCT UMR 6030 - CNRS - Université Caen-Normandie - CEA
Centre Cyceron
bd Becquerel
14074 Caen cedex
France
33.2.31.47.01.32
[email protected] <mailto:[email protected]>
http://www.istct.cyceron.fr/
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Dr. Nathalie Colloc'h
équipe CERVOxy
ISTCT UMR 6030 - CNRS - Université Caen-Normandie - CEA
Centre Cyceron
bd Becquerel
14074 Caen cedex
France
33.2.31.47.01.32
[email protected]
http://www.istct.cyceron.fr/
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--
Vincent Chaptal, PhD
Director of GdR APPICOM
Drug Resistance and Membrane Proteins Lab
MMSB -UMR5086
7 passage du Vercors
69007 LYON
FRANCE
+33 4 37 65 29 01
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