[cmview-devel] Fwd: pdb-l: New software tool RINalyzer for protein structure-function analysis

[Dan Bolser]

On 19 May 2011 16:00, Michael Lappe <drmlappe at googlemail.com> wrote:
> Had seen that, now I added a link to rinalyzer on my - aeeh - blog
> (see software) :
> http://cistronic.wordpress.com/
> OWL & cmview were already there.
> Any feedback is very much welcome! Thanks - .\\ichael
>
> BTW, I gathered a few lines on the CMview installation - Mainly bio.cc
> is down, but the mirror links still work.
> plus a few suggestions - Should I post them here or on the cmview bugtracker?
>
> @henning: still reading - ping me anytime.
>
> @jose: Could you remind me of the last paper you presented on a group-meeting?
> I remember you were very happy with the content along the lines of
> "Why didn't I read this earlier?"
>  - I am looking for the next paper to discuss on F1000.
>
> @dan: I guess you saw this - what's your take? network ensemble sounds
> good, is it worth digging through?
> http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001105;jsessionid=3ABA64B96A2138573730A8F2F9962087.ambra02

Heh... I don't read papers these days ;-)

Also, I've never read a microarray paper that I could understand, so I
don't think my opinion would mean much here. I'll pass it to the guy
in the lab who is very good at microarrays, and see what he thinks.

I'll keep an eye on your blog. Unfortunately, mine isn't very
interesting! http://bioblog5000.blogspot.com/


All the best,
Dan.

> On Thu, May 19, 2011 at 3:21 PM, Dan Bolser <dan.bolser at gmail.com> wrote:
>> I guess you guys have seen this... looks good, but not as powerful as cmview?
> I guess the added benefit comes from using all the plugins available
> for cytoscape,
> like calculating all the different graph-properties with it ...
>
>>
>> Perhaps you should do a link exchange?
>>
>>
>> Cheers,
>> Dan.
>>
>> ---------- Forwarded message ----------
>> From: Mario Albrecht <info at mario-albrecht.de>
>> Date: 19 May 2011 14:01
>> Subject: pdb-l: New software tool RINalyzer for protein
>> structure-function analysis
>> To: pdb-l at rcsb.org
>>
>>
>> Dear colleagues,
>>
>> RINalyzer allows the interactive analysis and visualization
>> of residue interaction networks (RINs) derived from
>> 3D protein structures. For each RIN loaded into the
>> network visualization software Cytoscape, the corresponding
>> molecular 3D structure is displayed simultaneously in UCSF Chimera.
>>
>> RINalyzer provides a number of valuable methods to identify
>> structurally and functionally important protein residues and
>> to explore the impact of residue substitutions. RINalyzer also
>> computes a comprehensive set of weighted network centrality
>> measures and supports the comparison of protein structures.
>>
>> In addition, the command-line tool RINerator can be used
>> to generate RINs from protein structures in the PDB.
>> Precomputed RINs are available for download from RINdata.
>>
>> RINalyzer works as plugin with Cytoscape 2.7.x and 2.8.x.
>>
>>
>> Further information and video tutorials can be found at:
>> http://www.rinalyzer.de/
>>
>> Press release:
>> http://www.idw-online.de/en/news423886
>>
>> Please use the following reference for citing our work:
>>
>> Doncheva, N.T., Klein, K., Domingues, F.S., Albrecht, M. (2011)
>> Analyzing and visualizing residue networks of protein structures.
>> Trends in Biochemical Sciences, 36(4):179-182.
>> http://dx.doi.org/doi:10.1016/j.tibs.2011.01.002
>>
>>
>> If you have any questions, comments or suggestions,
>> do not hesitate to contact us:
>> rinalyzer [at] mpi-inf [dot] mpg [dot] de.
>>
>> Kind regards,
>>
>> Nadezhda Doncheva
>> Francisco Domingues
>> Mario Albrecht
>>
>>
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>