Dear James,
I'll second Manferd's post.
We have a membrane protein that crystallizes with a continuum of cell
dimensions, so different that you can't merge the data to reach full
completeness, but you could manage to gain MR solutions for some
discrete states of the continuum and ending up in
Dear Jasmine,
I have a few questions about this bit:
//
As some users pointed out, single NAG could be just a part of the glycan that
the author chose to build, as most natural N-glycans must have stem of a common
core of 5 monosaccharides or its fucosylated version, such as those modeled in
th
Dear All
After about 10 (!) years of (very) hard work we solved the structures of our
dearest membrane transporter. Dataset at 2.9 And resolution, fairly
anisotropic, experimental phasing, and many long nights with Coot and
Buster to achieve model refinement.
The experimental structure h
on the day the news came out, I did wonder if the AlphaFold2 team somehow had
access to all the preliminary PDB files sent around via Gmail (which belongs to
the same company), but more as a joke/conspirational thought.
"our" target T1052, was also predicted very well by domains and as a monomer.
i think the answer to all these doubts and questions is quite simple: the
AlphaFold2 people must make all details of their methods public (source code)
and, as would probably be necessary, open their system for inspection and use
by independent experts. isn't that what peer review and reproducib
It seems immensely powerful, but my impression is it shows just how much
information can be extrapolated from the PDB if a technique that can make use
of "deep similarity" can be employed.
Obviously alphafold2 can make use of relationships that arent limited to direct
homology, but if there is
Hi
Actually, since Deep Mind is a commercial organization (funded by shareholders
and people who buy their services), I don’t think they are subject to the same
rules as academia as regards making their source code public. It would be very
nice if they would (could?) make their code public, but
On Dec 9, 2020, at 07:16, Harry Powell wrote:
>
> ...the important thing is [...] they’ve done something that no-one else has
> managed to do as well in spite of years of trying.
What, precisely, is the “something”?
Exactly how much better than second place?
Was the scoring the same across al
The “something” is what gives them their edge (and which they’ve hinted at, but
avoided being explicit)…
The main quality score used to distinguish their results is GDT_TS (Global
Distance Test - Total Score - you can look it up on Wikipedia like I did).
Although it doesn’t say in Wikipedia, it
>they can maintain an advantage through several routes - they can
> publish in patents (so people can see what they’ve done, but not legally
> implement it )
In Europe and I think some other countries, inventions can only be patented
if they have *industrial applicability.*
In any case, acad
> On Dec 9, 2020, at 07:45, Harry Powell - CCP4BB
> <193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote:
>
> ... GDT_TS (Global Distance Test - Total Score - you can look it up on
> Wikipedia
Thanks, this is helpful.
Wikipedia:
“The primary GDT assessment uses only the alpha carbon atoms.”
Dear All
There is a 43kd protein purified via Ni-chelating affinity
chromatography, anion exchange chromatography and gel filtration chromatography
in sequence. However the chromatogram obtained showed an extremely asymmetric
peak shape. The aggregation forms of proteins are mainly in th
Salt concentrations less than 100 mM can lead to nonspecific adsorption to
the gel exclusion media, potentially leading to band broadening, and
delayed elution. Overloading gel exclusion columns (more than 2-4% Vt) can
also lead to elution band artifacts. Check these issues first.
Roger Rowlett
G
Hello, I agree with Roger, you should definitely try to increase the salt
concentration to get rid of non specific binding impurities. And if that
doesn't work, you can try purifying your protein under denaturing
conditions by adding one refolding step in the column.
Good luck,
Javier
On Wed, Dec
Dear Robbie,
In the case that only single monosaccharide was modelled at
glycosylation site with a known oligosaccharide sequence, technically
the software cannot generate glycosidic linkages, linear descriptors for
sequences, 2D SNFG images, etc. Therefore, this single monosaccharide
cannot
It would be sensible to analyse the state of your purified protein further.
* (SEC in reasonable salt conc containing buffer – this is standard
practice)
* Analytical ion exchange of purified protein - are there different states?
* SEC (in reasonable buffer) in line with MALS – is th
Hi,
A postdoctoral position is currently available in the Structural Chemistry
group, part of the Institute for Applied Cancer Science (IACS) within the
Therapeutics Discovery Division of MD Anderson Cancer Center. Our mission is to
integrate novel biological insights with drug discovery expert
Probably a good idea to share an image :) worth many words...
Artem
On Wed, Dec 9, 2020, 9:17 AM wrote:
> Dear All
> There is a 43kd protein purified via Ni-chelating affinity
> chromatography, anion exchange chromatography and gel filtration
> chromatography in sequence. However the c
Good thoughts, although there are always exceptions. For example, if a crystal
contact is mediated by an extended domain that is capable of adopting multiple
conformations (due to elbow motion, for example), then it may allow multiple
crystal forms. It happens a lot in RNA crystals, but can also
Dear Jasmine,
thank you for this explanation. It's the best explanation of this
remediation I've read.
The use of IDs may confuse people, so I'd like to reiterate it and ask
for clarification.
Every residue in the mmCIF format has three (3) independent chain IDs
assigned to it (and three sequence
Exactly. Without a picture of SEC profile it's even difficult to decipher the
meaning of "extremely asymmetric peak shape".
Beside that, one domain or multi-domain protein, extended N-term or C-term
loops containing constructs, column, load (weight & vol) and flow rate - any
one of these could a
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