Dear all,
Just commenting that after the stunning performance of AlphaFold that uses AI
from Google maybe some of us we could dedicate ourselves to the noble art of
gardening, baking, doing Chinese Calligraphy, enjoying the clouds pass or
everything together (just in case I have already
Dear all,
seems like one just needs to complain about it... It works again ;)
Thanks to all who replied!
Cheers,
Johannes
Am Do., 3. Dez. 2020 um 15:54 Uhr schrieb Jon Cooper <
jon.b.coo...@protonmail.com>:
> Works for me. Cheers, Jon.C.
>
>
> Sent from ProtonMail mobile
>
>
>
>
Dear Zhijie,
In generally I like the treatment of carbohydrates now as branched polymers. I
didn't realise there was an exception. It makes sense for unlinked carbohydrate
ligands, but not for N- or O-glycosylation sites as these might change during
model building or, in my case, carbohydrate
Job Summary:
A postdoctoral position in structural biology is available in the Center
for the Genetics of Host Defense at UT Southwestern Medical Center at
Dallas. Using forward genetics, the lab identifies many proteins and
protein complexes that have novel functions in the immune system,
Dear all,
I cannot access the ccp4 downloads webpage from my institute's pc or
mobile.
Is it just me? Is it a known problem? I get a 502 Proxy Error.
http://www.ccp4.ac.uk/download/
Cheers,
Johannes
To unsubscribe from
Hi all,
I was confused when I saw mysterious new glycan chains emerging during PDB
deposition and spent quite some time trying to find out what was wrong with my
coordinates. Then it occurred to me that a lot of recent structures also had
tens of N-glycan chains. Finally I realized that this
Hello. A quick look suggests that a lot of the test structures were solved by
phaser or molrep, suggesting it is a very welcome improvement on homology
modelling. It would be interesting to know how it performs with structures of
new or uncertain fold, if there are any left these days. Without
A quick note regarding the code that Deepmind released for CASP13 (2018).
It bears the rather important caveat that: "This code can't be used to predict
structure of an arbitrary protein sequence. It can be used to predict structure
only on the CASP13 dataset (links below)."
Source:
Hello,
we had a 124 aa target in Casp14, without any detectable homology to a known
structure. Within the experimental errors, the AlphaFold2 model is identical to
the NMR model we got. That was very convincing.
Best wishes
Wim
De: "Jon Cooper"
Dear Colleagues,
I would like to bring to your attention the Fully-funded PhD studentships
sponsored by the Doctoral School at Nottingham Trent University (deadline 4th
Jan 2021).
The PhD Programme is open to UK and non-UK applicants and information about the
eligibility criteria and the
Thanks for the advice Pavel!
I don't want to celebrate prematurely, but I just re-ran the same
refinement in both the stable and in nightly 4070, and it _seems_ to be
corrected in the nightly. Will let you know if it pops up again.
- Igor Petrik, PhD
On Thu, Dec 3, 2020 at 9:16 AM Pavel
Thanks Nigel,
I will put together the input and output file from my latest refinement and
send them to you and Pavel later today.
- Igor Petrik, PhD
On Wed, Dec 2, 2020 at 9:46 PM Folmer Fredslund wrote:
> Dear Igor
>
> There's a phenix bulletin board for question like this, which is where
Just curious, how does the result of the Phaser run with the Alphafold model compare with a Phaser run using the Arcimboldo phased model as a probe?
Boaz
Boaz Shaanan, Ph.D.
Department of Life Sciences
Ben Gurion University of the Negev
Beer Sheva
Israel
On Dec 4, 2020 00:32, Anastassis
It is a major leap forward for structure prediction for sure. A hearty
congratulations to all those teams over all those years.
The part I don't understand is the accuracy. If we understand what
holds molecules together so well, then why is it that when I refine an
X-ray structure and turn
?Does anyone know how AlphaFold performs on sequences with little conservation?
Virus and phage proteins are like this. Their structures are homologous, but
sequence identity can be less than 10%.
Reza
Reza Khayat, PhD
Associate Professor
City College of New York
Department of Chemistry and
Although they can now get the fold correct, I don't think they have all the
side chain placement so perfect as to be able to predict the fold and how a
compound or another protein binds, so we can still do complexes. I don't know
what others end up spending their time doing, but much of my work
Hello Jon,
We had a novel structure and it did very well. I haven't tried the MR to see if
the model would work, but it was so close that I can't imagine it not working.
Our protein was ~185 residues and the closest PDB structures were about 4
Angstrom rmsd over about 70 residues over just one
AlphaFold - or similar ideas that will surface up sooner or later - will beyond
doubt have major impact. The accuracy it demonstrated compared to others is
excellent.
“Our” target (T1068) that was not solvable by MR with the homologous search
structure or a homology model (it was phased with
I agree completely Tom. Having been recently involved in some efforts to
identify interesting compounds against SARS-CoV-2, I can say that the current
AI/ML methods for docking/predicting small molecule binding have very very low
success rates (I’m being generous here), even when you are
Thanks all, very interesting, so our methods are just needed to identify the
crystallization impurities, when the trays have been thrown away ;-
Cheers, Jon.C.
Sent from ProtonMail mobile
Original Message
On 3 Dec 2020, 22:31, Anastassis Perrakis wrote:
> AlphaFold - or
CC: pdb-l
Dear Zhijie and Robbie,
I agree with both of you that the new carbohydrate chain assignment convention
that has been recently adopted by PDB introduces confusion, not just for
PDB-REDO but also - and especially - for end users.
Could we kindly ask PDB to improve consistency by
Hello James, that's really strange - I've used refmac et al., to do poor man's
energy minimizations of models and they've generally come out fine, unless the
restraints, etc, are wildly off-target. I wasn't playing with X-ray weights
though, since there never was a dataset, of course.
Cheers,
I'm curious how well AlphaFold would do on an Intrinsically Disordered Protein
(IDP),
would it recognize that it is an "IDP" or predict that it has a structure (or
structures)?
It would be interesting to test such a sequence and see what comes out.
Possibly AlphaFold might be the best IDP
Hi everybody,
As one of the persons playing with the CASP14 data before all news came
out, I can answer some of the questions raised in this thread.
- "Does anyone know how AlphaFold performs on sequences with little
conservation?"
One of the things we looked at was how the accuracy of
We also recently encountered this way of coordinates treatment - did not
find it useful but just left it as it was (life has other more exciting
adventures waiting ...).
I strongly support the solution suggested by Luca,
A nice day to all,
Jan Dohnalek
On Fri, Dec 4, 2020 at 8:48 AM Luca
Hi,
Dr Nicholls brings up many interesting points, but doesn't touch on
the major point I had hoped to make in my letter. Whenever you start
making multiple tests of your hypothesis you have to evaluate each of
those tests with a higher standard than you would if you only applied
one.
Hi Dale,
You're absolutely right - the multiple hypothesis testing problem is one that
is often not considered, let alone properly accounted for. Whilst this can be
accounted for by appropriate adjustment of significance levels when a known
number of explicit hypotheses are tested (and when
A way to achieve a feeling for the significance of the different map
features that you are looking at in your current project, is the old
control technique to omit both a well ordered part of the model
(residue, alpha-helical turn, part of a beta-strand, ...) and a less
well ordered part
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