HI,
I simply opened this in Pymol, saw the non designated structed, typed dss
(https://www.pymolwiki.org/index.php/Dss) and then saw the secondary
structure...
It "may" be that it is not designated in the pdb file (however I haven't
looked).
J
From: CCP4 bulletin board On Behalf Of Firdous
Dear Harry, you can run alphafold via
https://colab.research.google.com/github/deepmind/alphafold/blob/main/notebooks/AlphaFold.ipynb#scrollTo=woIxeCPygt7K
*Cited*
*"Differences to AlphaFold v2.0*
In comparison to AlphaFold v2.0, this Colab notebook uses*no templates
(homologous structures)*a
lDDT = Local Difference Distance Test, for reference...
Harry
--
Dr Harry Powell
> On 17 Aug 2021, at 20:21, Randy John Read wrote:
>
> What the DeepMind people say about this is that when part of a predicted
> structure has a low predicted lDDT (a CASP measure of model quality), this is
> a
What the DeepMind people say about this is that when part of a predicted
structure has a low predicted lDDT (a CASP measure of model quality), this is a
good indicator that it may be intrinsically disordered.
Best wishes,
Randy Read
> On 17 Aug 2021, at 17:13, Sorin Draga wrote:
>
> Dear al
Dear Colleagues:
My laboratory at the University of Texas Health Science Center at San
Antonio is seeking an enthusiastic Postdoctoral Fellow to work on an
NIH-funded project on SARS-CoV-2 and RNA modification. We will use X-ray
crystallography, cryo-EM, and cell-based methods to address basic
me
Dear Harry,
Thanks very much for the info about RoseTTAFold. As for AlphaFold, there are
ways to run it through Google Colab e.g. https://t.co/kxvjLVFwQx
I’d also advise against using these for IDPs.
Best wishes
James
On Aug 17, 2021, at 17:13, Harry Powell - CCP4BB
<193323b1e616-dmarc-re
Dear all,
Regarding the AlphaFold2: while its results are impressive for properly
folded proteins, I would caution against using it for IDPs: they do not
have a stable 3D structure that can be predicted, instead they occupy an
ensemble of structures, with a high degree of heterogeneity. While you
Hi
Forgive me if I’ve missed something, but I can’t find a way to run AlphaFold
without installing it locally - in which case I need a reasonable GPU.
On the other hand, RoseTTAFold does pretty much the same thing and is available
via David Baker’s web server - upload your sequence and sit back
As Joel has suggested before, alphafold on an IDP would be interesting
and would seem like a zero-cost starting point - perhaps one you have
tried already.
Sent from ProtonMail mobile
Original Message
On 15 Aug 2021, 15:53, Scott Horowitz < scott.horow...@du.edu> wrot
Hi,
As far as I recall (and I could well be wrong/not uptodate) Chimera reads the
SS description on the input PDB and implements them. So you could perhaps edit
the pdb to have the correct descriptions, as you wish.
My 2p contribution.
Boaz
Boaz Shaanan, Ph.D.
Dept. of Life Sciences
Ben Gurion
Hello, only other thought was that malonate might be binding in two
conformations, i.e. dual occupancy, and did you use a protease inhibitor
cocktail, since the constituents can react? The density looks a bit like
citrate, but too close to the His. I couldn't read the distances to the His in
yo
Hi Jon,
Thanks for the reply. I don't think this is acetylation, because I only see
this density in the crystals that grew with malonate. In other conditions
doesn't show anything like that. So I thought it'd be the malonate. But
I'll check on that.
Thanks for the suggestion.
Kind regards
Ana
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