[ccp4bb] COVID-19 - help design protease inhibitors - 1st round Thurs midnight

[Frank Von Delft]

To all you structural biologists locked out of your labs, bored with answering 
emails or writing your non-COVID paper, and itching all your lives to be 
medicinal chemists, here's your chance:

https://covid.postera.ai/covid

And you get to do something directly on COVID too.

It's easy:

  *   stare at the pile of fragments we found bound to the SARS-CoV-2 Main 
Protease in our somewhat epic XChem fragment 
screen
 this month (alluded to by others)
  *   see if you can spot cool ways of (especially) merging those hits - or 
anything else
  *   draw the compound onto that page
  *   hit submit

It's actually a bit harder than it sounds - so we're betting that many brains 
will crack the nut of hitting potency in one go (!).

We will do the rest - well, we'll try, if the Filters Approve and the Funds 
Permit -- and even for that, you can contribute, or tell people that could 
contribute (details on that page).

First collection closes tomorrow (Thurs) midnight Pacific Time (but there will 
be more).


Yes, it is a huge social experiment and a total crapshoot - but we must do 
something!  So thank you for all and any help...

*** Do forward to anybody relevant, especially experienced medicinal chemists.

*** If you know virology labs set up to do SARS-CoV-2 assays, email the address 
on that page.

*** If you have help to offer or wisdom to share, do so on the forums on that 
page

*** If you want to use the data for anything else - PLEASE DO - we were anxious 
to push it out ahead of PDB release cycle or getting preprint written.


Frank


--
Prof Frank von Delft
Professor for Structural Chemical Biology

Principal Beamline Scientist: I04-1 and XChem
Diamond Light Source
+44 1235 778997 (office: M,T,T)
+44 7471 026103 (mobile)

Principal Investigator: Protein Crystallography
Structural Genomics Consortium
Oxford University
+44 1865 617583 (office: W,F)





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[ccp4bb] Postdoctoral position in Structural Biology of Lysine methylation and Cancer in Grenoble

[Montse Soler Lopez]

Dear all, 

on behalf of Jan Kadlec from the Institute of Structural Biology (IBS)
in Grenoble, France: 

POSTDOCTORAL POSITION IN STRUCTURAL BIOLOGY OF LYSINE METHYLATION AND
CANCER IN GRENOBLE 

A 2-year post-doctoral position is available in the laboratory of Jan
Kadlec at the Institut de Biologie Structurale (IBS) in Grenoble, France


The project is focused on structural and biophysical characterization of
non-histone targets of lysine methyltransferases involved in cancer
development. The aim is to understand the mechanism by which the
methylation of these new substrates causes cancer to eventually develop
novel anti-cancer therapeutics.   

The project will be carried out in collaboration with the Reynoird team
(IAB Grenoble, nicolas.reyno...@univ-grenoble-alpes.fr,), expert in
lysine methylation signaling (see Reynoird et al., Genes Dev. [1]  2016
and Mazur*, Reynoird* et al. Nature. 2014). Another 2-year postdoc
position in lysine signalling is avalilable in his lab and both postdocs
will work together on different aspects of the project. 

Our group is specialized in structural analysis of epigenetic
regulators. We use an interdisciplinary approach combining structural
biology (X-ray crystallography, EM, NMR), biochemistry, cell biology and
mass spectrometry. 

The IBS is a member of the Partnership for Structural Biology
(www.psb-grenoble.eu [2]) providing access to integrated
state-of-the-art structural biology technologies, including ESRF
synchrotron X-ray beamlines for MX and SAXS, cryo-EM/tomography and NMR
as well as biophysics, confocal microscopy and high-throughput
crystallization platforms. 

The successful candidate will be highly motivated and have recently
acquired a PhD in the field of biochemistry/structural biology. Skills
in protein sample preparation methods (protein expression and
purification) are required and experience in protein crystallography
would be an advantage. 

Preferable start: June 2020. 

Informal inquiries and applications including CV and names of two
possible referees can be sent directly to Jan Kadlec (jan.kad...@ibs.fr)
by May 1st. 

Links:
--
[1] https://www.ncbi.nlm.nih.gov/pubmed/26988419
[2] http://www.psb-grenoble.eu



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[ccp4bb] Beta Test the Next Generation RCSB PDB website at http://beta.rcsb.org

[Christine Zardecki]

Test drive significantly revised and updated tools for searching and exploring 
PDB data at http:// beta.rcsb.org 
 before this new site is moved into production in April.
Improved and enhanced tools include:

Basic Search available from the search box at the top of every page
Advanced Search Boolean options 
Display of Advanced Search results for PDB structures, assemblies or unique 
polymeric molecular entities (unique sequences)
Structure and Sequence Similarity and Annotation Browsing integration in 
Advanced Search
Left-hand menu for refining Search Results 
Stored Search History
New MyPDB features: registration via Google/Facebook/ORCID authentication; 
save/rerun/receive email notifications of searches
Improved Download Tool for batches of data files
New GraphQL and REST APIs for data access and searching
Please note some RCSB PDB features are still in development but will be made 
available soon, including Custom Tabular Reports and a Chemical Component 
Search tool.

Your feedback will help ensure RCSB PDB services support our users. Please use 
the orange Contact Us button on the middle of the right-hand side of each page.



--
CHRISTINE ZARDECKI
Deputy Director, RCSB Protein Data Bank
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Road, Piscataway NJ 08854
P: 848.445.4924 | E: christine.zarde...@rcsb.org 






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Re: [ccp4bb] Coot under WSL2

[Clement Degut]

Update to my update

It is possible to have coot fully functional under WSL2 with the native
openGL on.
The caveat is :
- You need a full linux desktop environment installed (xfce4 for me)
- You need to use the host X server (VcSrv in my case) as single window, so
you lose a bit of the seamless integration with windows in that case, but
you have to do that only with coot (or any openGL software)
after starting the DE, coot will work normally with very decent speed, the
upcoming direct hardware access for the VM may also improve performance.

In these conditions full CCP4 (or everything I tried at least) can work
relatively seamlessly in windows while using the linux version.
(it actually works better than the actual windows version imho)

Clément


On Thu, 19 Mar 2020 at 14:56, Clement Degut 
wrote:

> Immediate update :
>
> If you use VcXserv, you need to start it with all default option, and
> generate a config file.
> Then change in the file wgl to False.
> Restart computer (yes)
> And start VcXserv with the modified config.
> If you simply deactivate native openGl via the gui nothing is working
> anymore for some reason, it must change another option somewhere.
>
> doing that the display of coot is perfectly fine, just a bit laggy, as i
> guess it's full software render, but usable (with a beefy CPU).
>
> Clément
>
> On Thu, 19 Mar 2020 at 14:48, Clement Degut 
> wrote:
>
>> The performance are massively improved in WSL2 versus WSL1, so maybe it's
>> why you had bad memory of it ?
>> WSL2 is currently only available in insider fast ring, but will be for
>> everyone with next major update (v2004) in few weeks.
>>
>> The main problem is, while you can use the right toolbar by simply
>> detaching it, selecting residues is almost impossible as the pointer is
>> still using the main UI as reference, but the 3D display  is away, so you
>> need to click far from the residus you try to select.
>>
>> I am playing around with the xserver options, but am not sure what I am
>> doing with that windows X server.
>> I'll update if I find a solution.
>>
>> Clément
>>
>> On Thu, 19 Mar 2020 at 13:31, Paul Emsley 
>> wrote:
>>
>>> On 19/03/2020 12:43, Clement Degut wrote:
>>> >
>>> > I have been recently trying to use ccp4 in windows subsystem for Linux
>>> 2 (Ubuntu distribution), everything i
>>> > tried run perfectly smoothly, including graphical interfaces.
>>>
>>> I am pleasantly surprised - when I tried that (some time ago) the
>>> graphics performance as terrible. Perhaps
>>> you have better hardware.
>>>
>>> > My only problem is with coot (latest build), the interface is working
>>> fine, as well as the 3D graphical. The
>>> > only problem is that the graphical window is offset from the rest of
>>> the UI (see screenshot).
>>> > So although it looks like everything would work smoothly it's not
>>> really usable.
>>>
>>> What, would you say, is the biggest problem?
>>>
>>> > I guess it comes from the absence of GPU access under WSL2 and so no
>>> proper display driver, but does anyone
>>> > had this problem? (and managed to solve it).
>>>
>>> FWIW, I have not seen this problem before (and don't know how to fix it)
>>>
>>> It seems to me an X server problem (or configuration issue). Have you
>>> tweaked or disabled the native OpenGL
>>> options on the X server?
>>>
>>> > Would be very useful for people working from home without a full linux
>>> dual boot.
>>>
>>> Hmm.
>>>
>>> > In a more general note, it seems that WSL2 will be able to replace
>>> windows specific build very effectively
>>> > in the very near future.
>>>
>>> For everything other than OpenGL graphics (and maybe the Cloud would
>>> also be problematic), yes, it seems so.
>>>
>>> Paul.
>>>
>>



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