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
>
