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 <[email protected]>: > Hi Claudia, > > another program that I used with success is Hollow ( > https://www.ncbi.nlm.nih.gov/pubmed/19014592). > It is really easy to use. You can get is here 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 <[email protected]>: > >> 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" <[email protected]> wrote: >> >> Hi Claudia, >> >> Another possibility is CastP: 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: >> [email protected] <[email protected]> Phone: 972-8-647-2220 Skype: >> boaz.shaanan Fax: 972-8-647-2992 or 972-8-646-1710 * >> >> >> >> >> >> >> >> ------------------------------ >> *From:* CCP4 bulletin board <[email protected]> on behalf of Claudia >> Binda <[email protected]> >> *Sent:* Tuesday, January 30, 2018 1:51 PM >> *To:* [email protected] >> *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. 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 <+39%200382%20985535> >> Fax: +39-0382-528496 <+39%200382%20528496> >> E-mail: [email protected] >> 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: [email protected] Web: http://www.unipv.it/biocry
