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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
Hi all,
I should mention 2D-GraLab which is a nice program (you must register to
download it) to display in 2D and analyze (a little bit as LigPlot)
interactions between two chains within a structure.
I have verified the data outputs for several interacting partners using
a different program.
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
Thank you all for your valuable suggestions. They have really worked well for
me :)
Regards,
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
As I'm sure you've also found, it's not simple to find one [easily
accessible] program that examines and reports every type of
interaction that might be of interest to you. So I'm sending in a
reference to another web-based tool that I've found complementary to
PISA and the others mentioned here.
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
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.
Dear Debasish,
Unless I have misunderstood your query this is very much on-topic and
sounds a lot like the sort of thing PISA is designed to give you. See
http://www.ccp4.ac.uk/html/pisa.html
Cheers
-- David
On 10 March 2015 at 10:25, Debasish Kumar Ghosh dkgh...@cdfd.org.in wrote:
Dear All,
Dear Debasish,For GUI try Pymol, Chimera, CCP4MG.Also try CCP4-CONTACT not an
GUI, but you get all possible interactions between two chains.best wishesÂ
S.M.Jaimohan, Ph.D
On Tuesday, 10 March 2015 3:58 PM, Debasish Kumar Ghosh
dkgh...@cdfd.org.in wrote:
Dear All,
Apologies for
Hi,
PDBsum (http://www.ebi.ac.uk/pdbsum/) can also analyze and make a summary
of interactions between partners of a protein-protein complex. Just submit
your pdb by clicking the 'generate' option from the left menu on the main
page.
Best,
Gulcin Gulten, Ph.D.
On Tue, Mar 10, 2015 at 11:57 AM,
Dear Debasish,
The WHAT IF software can do some things for you. As you probably don't
want to install a thirty year old package just for some inter-chain
contacts, I added a server for you to the WHAT IF servers that are
available at http://swift.cmbi.ru.nl/ look under contacts, it is the
bottom
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