Dear all,
The Reinherz lab at Dana-Farber Cancer Institute and Harvard Medical School is
recruiting a postdoctoral fellow to study HIV-1 vaccine development. The
successful candidate will enjoy working in a dynamic and collaborative research
environment focused on structural/molecular
I guess you did test P3 P31 and P32?
E
On Fri, 11 Dec 2020 at 17:19, Schreuder, Herman /DE <
herman.schreu...@sanofi.com> wrote:
> Hi Suraj,
>
>
>
> It is strange that the P3 crystals do not produce a MR solution. Since
> they all came from the same crystallization condition, you may want to
>
Dear All
we are currently off line. The water cooling is undergoing maintenance where
our servers sit. We had hoped to continue to run downloads,etc, but it looks
like the front-end machine has gone down. Planned return to normal is 9 am
GMT, this is if the front-end shutdown was a planned
Hi Suraj,
It is strange that the P3 crystals do not produce a MR solution. Since they all
came from the same crystallization condition, you may want to check that no
proteolytic cleavage of your protein has taken place and that your crystals
only contain a fragment of your protein. You may
In reply to James, BLAST will align sequences but your premise is that
the function of the 'unknown' sequence/structure is the same as that of
the 'known'. The lipocalin family is one which has a wide distribution
and the functions vary considerably from involvement with embryo
implantation to
Well, that problem was solved a long time ago. An excellent
function-from-sequence predictor is here:
https://blast.ncbi.nlm.nih.gov/Blast.cgi
AlphaFold2 is doing rather much the same thing. Just with a 3D output
rather than 1D, and an underlying model with a LOT more fittable parameters.
Hello everyone,
The NCI RAS Initiative at Frederick National Laboratory for Cancer Research
is looking for a Scientist with experience in biophysics and structural
biology. The candidate will join my group and be responsible for the
structural characterization of protein-protein and
Thanks, I will try this.
Also, on CASP website there are such scores as RMS_ALL (can be seen in
tables) and GDC_SC (for side-chains, not visible in tables for some reason).
RMS_ALL presumably includes side-chains and seems good for AlphaFold2
models, between 1 to 2 Angstrom (apart from the
Hello, have you tried the 'pointless' option to use one of the
structures/datasets as a reference, then there should not be a need to do MR on
the others, since they will all be indexed consistently. Sorry if that is what
you meant below. Cheers, Jon Cooper.
Sent from ProtonMail mobile
Well - C2 is a sub cell for P3 so that isnt surprising, but a cell
difference of 202 to 212 means it isnt isomorphous..
But an
Rw Rf/ of 26/31 isnt bad for such low resolution data?
Eleanor
On Fri, 11 Dec 2020 at 12:01, Suraj Kumar mandal
wrote:
> Dear Sir,
>
> Yes, we have checked handedness
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
> 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:
I agree with Phil!
Yes, it is nice to be able to obtain better models but interesting biological
function resides usually in the most variable and least predictable features of
a protein, how it associates with other proteins etc. Even when a fold can
predicted, such folds alone frequently
Dear Jasmine,
I fully agree with this recommendation:
> To use the wwPDB-assigned chain ID in publications,
> _atom_site.auth_seq_id _atom_site.auth_comp_id, and
> _atom_site.auth_asym_id can be used for the residue number, residue ID,
> and chain ID, respectively.
It would help a lot if the
Alpha-fold looks great and is clearly a long way towards answering the question
“this is the sequence, what is the structure?”
But I’ve always thought the more interesting question is “this is the
structure, what does it do?” Is there any progress on that question?
Phil
> On 11 Dec 2020, at
I see, thanks, that looks good.
Where can one download predicted_model+exp_model PDBs together?
I could easily find predicted models but not experimental - CASP website
seems very cryptic.
Also, can you comment on how much GDT_TS depends on CA and how much on
side chains positioning?
E.g.
I'm not Randy, but I do have an answer: like this. This is T1049-D1. AlphaFold
prediction in red, experimental structure (6y4f) in green. Agreement is close
to perfect, apart from the C-terminal tail which is way off - but clearly
flexible and only resolved in this conformation in the crystal
Dear Sir,
Yes, we have checked handedness also. We are using the same MR solution
with other data.
With best regards
Suraj
On Fri, Dec 11, 2020 at 4:56 PM srajan kapoor
wrote:
> Have you checked for handedness to solve this problem?.
> You can also try to use the structure that you have
Dear Madam,
All the data set have the similar cell dimensions. The only difference I
observe is that the data which gives solution in C2 space group has the
cell dimensions as a=140, b=80, *c=202*, alpha=beta=gamma=90.
We tried processing other data in C2 space group (forcefully) with cell
Do all data sets have similar cell dimensions.
P3i can be indexed in a variety of ways, (h k l ) (k,h,-l) etc - refer to
documentation on reindexing..
-
All *P3i* and *R3*:
(h,k,l) *not* equivalent to (-h,-k,l) *or* (k,h,-l) or (-k,-h,-l) so we
need to check all 4 possibilities:
So
Dear All,
We are trying to solve a structure of a protein, for which we have
collected five different home source data at 3.2-3.5 Ang resolution. We are
processing the data using iMOSFLM and the program suggests P3 (and related)
space groups for all the data. We are able to get a solution with
Dear Randy,
Can you comment on why for some of AplhaFold2 models with GDT_TS > 90
(supposedly as good as experimental model) the RMS_CA (backbone) is > 3.0
Angstrom? Such a deviation can hardly be described as good as experimental.
Could it be that GDT_TS is kind of designed to evaluate how
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