As this is a ccp4 bb we should mention the jsPISA server which is at
http://www.ccp4.ac.uk/pisa/
This is a very nice implementation of the PISA approach.
Another approach is to use the Chimera clash finding approach
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/findclash/findclash.html
But this defaults to atom to atom contacts which means you have to prune it
down with a script for picking residues. Also does not know about H-bond
angles
Cheers
Martyn
Cambridge
Original message
From : bar...@fmp-berlin.de
Date : 18/03/2015 - 14:18 (GMTST)
To : CCP4BB@JISCMAIL.AC.UK
Subject : [ccp4bb] Antw: Re: [ccp4bb] Offtopic: Software to closely visualize
interacting partnets in protein complex
Hi,
I just checked the PIC sever tim suggested. very nice indeed. If
you only want to map different interfaces and the amino acids involved
in, I suggest to run the pisa server, too. http://www.ebi.ac.uk/pdbe/pisa/ . I
used it extensively to find out whether a certain set of crystal contacs leads
to a certain crystal packing.
best, matthias
Tim tim.schu...@rub.de 11.03.15 18.25 Uhr
Hi,
Molprobity is also a nice software to do this kind of analysis - if you
use it as implemented in phenix you also get good visualization in coot.
I also asked the pymol community to create an implementation for pymol,
but I did not follow if somebody took that up.
Also this 'protein interactions calculation' server is very neat:
http://pic.mbu.iisc.ernet.in/
/Tim
On 10/03/15 11:25, Debasish Kumar Ghosh wrote:
Dear All,
Apologies for this little off-topic inquiry. I want to closely visualize the
interacting residues in an multimeric protein complex to understand the
nature of interactions. Is there any good software to give this information
with good clarity.
Any suggestion is highly appreciated.
Thanks,
Best !!!
Debasish Kumar Ghosh
CSIR- Junior Research Fellow (PhD Scholar)
C/o: Dr. Akash Ranjan
Computational and Functional Genomics Group
Centre for DNA Fingerprinting and Diagnostics
Hyderabad, INDIA
Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com
Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab)
Lab URL:
http://www.cdfd.org.in/labpages/computational_functional_genomics.html
