You can try VOIDOO as well:
http://xray.bmc.uu.se/usf/voidoo.html
a bit dated but still effective
Cheers, Fulvio
Il 01/02/18 09:54, Claudia Binda ha scritto:
Dear All,
thanks everyone for your help.
Below is a summary of all suggestions for calculating and representing
cavities of protein structures.
Best
Claudia
Caver (https://www.caver.cz/)
3V (http://3vee.molmovdb.org)
ProFunc (https://www.ebi.ac.uk/thornton-srv/databases/profunc/)
Ghecom (http://strcomp.protein.osaka-u.ac.jp/ghecom/)
using pymol with no other plug-ins required
CastP (http://sts.bioe.uic.edu/castp/index.html)
Metapocket (http://projects.biotec.tu-dresden.de/metapocket/)
Hollow (http://hollow.sourceforge.net/)
2018-01-30 14:55 GMT+01:00 Johannes Cramer <johannes.cra...@gmail.com
<mailto:johannes.cra...@gmail.com>>:
Hi Claudia,
another program that I used with success is Hollow
(https://www.ncbi.nlm.nih.gov/pubmed/19014592
<https://www.ncbi.nlm.nih.gov/pubmed/19014592>).
It is really easy to use. You can get is here
http://hollow.sourceforge.net/ <http://hollow.sourceforge.net/>
It finds pockets in a defined area, fills them with water
molecules and generates a pdb with those waters. You can then
import it into pymol and represent it however you think is fitting.
Cheers,
Johannes
2018-01-30 14:20 GMT+01:00 Vipul Panchal <panchal.vi...@igib.in
<mailto:panchal.vi...@igib.in>>:
Hi Claudia,
For the identification of cavities and residues linning them,
metapocket is one of the preferred choice as it uses
prediction from various program.
Output of the server is pdb file.
I found caver program represent cavities in a best manner.
There is caver plugin available for pymol. Output is tunnel
like representation with different colours. Interestingly, it
also provides tunnel length, radius and list of residues
linning the bottle-neck of each of the cavity. As a input for
the presentation of cavities, you need to provide list of
residues lining cavities. Identified by other programs.
All the best!
On 30-Jan-2018 6:28 PM, "Boaz Shaanan" <bshaa...@bgu.ac.il
<mailto:bshaa...@bgu.ac.il>> wrote:
Hi Claudia,
Another possibility is CastP:
http://sts.bioe.uic.edu/castp/index.html
<http://sts.bioe.uic.edu/castp/index.html>
They also have a Pymol plugin. I have not used this plugin
since I'm displaying the CastP o/p files in UCSF-chimera
which handles them nicely.
Cheers,
Boaz
/Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben-Gurion University of the Negev
Beer-Sheva 84105
Israel
E-mail: bshaa...@bgu.ac.il <mailto:bshaa...@bgu.ac.il>
Phone: 972-8-647-2220 Skype: boaz.shaanan
Fax: 972-8-647-2992 or 972-8-646-1710 /
//
//
/
/
------------------------------------------------------------------------
*From:* CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK
<mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of Claudia Binda
<claudia.bi...@unipv.it <mailto:claudia.bi...@unipv.it>>
*Sent:* Tuesday, January 30, 2018 1:51 PM
*To:* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>
*Subject:* [ccp4bb] cavities in protein structures
Hi everyone,
I need suggestions to calculate and represent cavities of
protein structures. For years I have been using Voidoo
that produces maps in ezd format which could be converted
in map format (ccp4) using the online server
http://xray.bmc.uu.se/cgi-bin/gerard/mapman_server.pl
<http://xray.bmc.uu.se/cgi-bin/gerard/mapman_server.pl>.
However, this does not work anymore. Is there another way
to do it? What is the best tool to calculate cavities and
draw them by Pymol or ccp4mg?
Thank you
Claudia
--
Claudia Binda
University of Pavia
Dept. Biology and Biotechnology
via Ferrata 1, 27100 Pavia - Italy
Phone: +39-0382-985535 <tel:+39%200382%20985535>
Fax: +39-0382-528496 <tel:+39%200382%20528496>
E-mail: claudia.bi...@unipv.it <mailto:claudia.bi...@unipv.it>
Web: http://www.unipv.it/biocr <http://www.unipv.it/biocry>
--
Claudia Binda
University of Pavia
Dept. Biology and Biotechnology
via Ferrata 1, 27100 Pavia - Italy
Phone: +39-0382-985535
Fax: +39-0382-528496
E-mail: claudia.bi...@unipv.it <mailto:claudia.bi...@unipv.it>
Web: http://www.unipv.it/biocry
