[ccp4bb] AW: [ccp4bb] Looking for method to find similar oligomeric arrangement

[Brandstetter Johann]

Topsearch does that, https://topsearch.services.came.sbg.ac.at/
Best,
Hans

Von: CCP4 bulletin board  Im Auftrag von Andrew Lovering
Gesendet: Sonntag, 21. Juni 2020 10:51
An: CCP4BB@JISCMAIL.AC.UK
Betreff: Re: [ccp4bb] Looking for method to find similar oligomeric arrangement


Thanks Boaz for the SSM heads up. I was much too DALI-centric!



One last point, if anyone can offer an opinion - I presume most methods will 
match but only within ASU contents.



Does any approach utilize deposited "biological unit" classification or (better 
still) crystallographic symmetry operators?



Best

Andy



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Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?)

[Brandstetter Johann]

Eventually computational methods (like AlphaFold) should provide reliable 
information on the spectrum of metastable conformational substates that a 
protein can adopt, i.e. its dynamics. This information will be valuable to 
answer the question of a protein's function, and also of its crystallization - 
and if it is only: difficult!

Best,
Hans

-Original Message-
From: CCP4 bulletin board  On Behalf Of Bryan Lepore
Sent: Freitag, 11. Dezember 2020 15:03
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] External: Re: [ccp4bb] AlphaFold: more thinking and less 
pipetting (?)

> On Dec 11, 2020, at 07:42, Phil Evans  wrote:
> 
> But I’ve always thought the more interesting question is “this is the 
> structure, what does it do?”

It sounds compelling though, that methods of the sort implemented in the CASP 
work are perfectly poised to make progress on the question:

“how might this protein crystallize?”

-Bryan W. Lepore


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[ccp4bb] nanodispenser Hydra II crystallisation robot

[Brandstetter Johann]

Dear colleagues,

we have problems to find a replacement for the protein nano-dispenser (needle) 
of our Hydra II crystallization robot which was previously distributed by the 
company Matrix, later taken over by Innovadyne, then by Thermo Fisher (who do 
no longer support the system).
For clarity, a photo of the nanodispenser needle can be seen here 
https://dl.dropboxusercontent.com/u/65420789/2015-04-23_Nano.pdf .

Thank you very much for suggestions where we might get a replacement of the 
nanodispenser,
Hans


--
Prof. Dr. Hans Brandstetter
Department of Molecular Biology
University of Salzburg
Billrothstr. 11
A-5020 Salzburg
phone: 0043 662 8044 7270
email: hans.brandstet...@sbg.ac.at
web: www.uni-salzburg.at/brandstetter