[ccp4bb] Scientific Data Curator position (PDB and EMDB)

[Deborah Harrus]

Dear all,

We are looking to recruit an expert structural biologist or 
bioinformatician to join the PDBe curation team on the Wellcome Genome 
Campus near Cambridge.


The work involves annotating preliminary PDB and EMDB submissions and 
extracting relevant biological information and will also involve 
analysis of structure data and enriching PDBe tools and services. The 
data curators also participate in developing training material and 
delivery of workshops and in outreach activities.


The closing date for this post is 12th September 2023.

For more information and to apply, visit:

https://www.embl.org/jobs/position/EBI02149

Kind Regards

Deborah Harrus

--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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[ccp4bb] Postdoctoral Position

[Krishna Chinthalapudi]

Dear All,



We are excited to announce the opening of a joint postdoctoral scientist
position in the laboratories of Dr. Sarah Heissler and Dr. Krishna
Chinthalapudi at the Ohio State University. This exceptional opportunity
focuses on groundbreaking research to unravel the role of myosin motors and
cytoskeletal proteins in both health and disease. Our approach combines
cutting-edge structural biology techniques, including cryo-EM and X-ray
crystallography, with biochemical, biophysical, and cell biological methods
to deeply investigate the structure and function of myosin motors, as well
as their regulation by cytoskeletal proteins.



Our laboratories are well equipped with state-of-the-art instrumentation
for the proposed studies and have generous access to a Titan Krios G3i
Cryo-TEM equipped with a BioQuantum imaging filter and a K3 direct electron
detector, imaging phase plates, and an image spherical aberration
corrector. In addition, our labs have access to a Glacios with a Falcon III
detector and a Ceta-D camera for MicroED analysis at the world-class Center
for Electron Microscopy and Analysis (CEMAS) at the Ohio State University.



To be eligible for this position, candidates must hold a Ph.D. degree and
possess considerable experience in structural biology. If you also have a
background in molecular biology techniques, and/or high-resolution imaging,
it would be highly desirable. To apply for this exciting opportunity,
kindly email us your CV, a short cover letter detailing your research
experience and interests, and the contact information for three references
to Sarah Heissler (sarah.heiss...@osumc.edu) and Krishna Chinthalapudi (
krishna.chinthalap...@osumc.edu).



Best,

Krishna



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[ccp4bb] RNA-Protein crosslinker

[Haaris Ahsan Safdari]

Hi everyone,

I was looking for an effective RNA-protein cross linker for one of my
project. I don’t intend to go down to UV cross linkers but any other
recommendations and suggestions are welcome.

Thanks and Regards
Haaris
-- 
Best regards,
Haaris Ahsan Safdari



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[ccp4bb] Job Advert: Drug Discovery Project Research Scientist position, Francis Crick Institute, London, UK.

[David Briggs]

Dear all,

We have a position available at the Francis Crick Institute - please share with 
any soon-to-finish PhD students and postdocs who might be interested:

We seek a talented, highly motivated and independent post-doctoral project 
research scientist to work on a project to design protein kinase C beta 
selective inhibitors for B cell malignancies. Work will be carried out in Neil 
McDonald's laboratory at the Francis Crick Institute, in collaboration with 
clinician-scientist Ingo Ringshausen at the University of Cambridge, and is 
funded by a Cancer Research Horizon Therapeutic Catalyst Award.

The project will be funded for 18 months in the first instance, with the 
potential for extension depending on progress.

The project will build upon prior work within our laboratory to characterise 
and develop new, selective kinase inhibitors. The work will involve both 
optimisation of existing inhibitors, and the parallel discovery of novel 
inhibitors using an XChem Fragment screening approach at Diamond Light Source.

The Francis Crick Institute is situated in central London, and is the largest 
single-site biomedical research institute in Europe, with excellent provision 
for X-ray crystallography and medicinal chemistry to allow rapid 
characterisation and follow-up of any lead compounds.

Prior experience with baculovirus protein expression and X-ray crystallography 
would be advantageous.

Informal enquiries can be made to Professor Neil McDonald 
(neil.mcdon...@crick.ac.uk).
Application Deadline: 1st Sept 2023.

For more details about the role and the application process, please see:

https://crick.wd3.myworkdayjobs.com/External/job/London/Postdoctoral-Project-Research-Scientist---Signalling-and-Structural-Laboratory_R1245-1



--

Dr David C. Briggs CSci MRSB (he/him)

Principal Laboratory Research Scientist

Signalling and Structural Biology Lab

The Francis Crick Institute

London, UK

Working hours: Mon-Fri 0900-1700

==

about.me/david_briggs | 
OrcID | Google Scholar 


The Francis Crick Institute Limited is a registered charity in England and 
Wales no. 1140062 and a company registered in England and Wales no. 06885462, 
with its registered office at 1 Midland Road London NW1 1AT



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Re: [ccp4bb] Connecting DNA between asymmetric units?

[Ronnie Berntsson]

Hi Phil,

Thank you, I appreciate the input. We’ll try a few more things. However, it 
seems that also in P1 we don’t really see a break in the DNA density (it slowly 
spirals in the crystal packing, as the protein bends it in between two protein 
monomers). My thinking is that this can be explained by the “sliding” nature of 
the bining, since there is no sequence specificity here (it’s a poly-A). We of 
course know that the DNA is 60 bases long, but my guess is that the breaks 
between strands occur in different sites in the crystal and therefore gets 
averaged out in the observed density. Just don’t really know how to properly 
handle it in the modelling.

In principle the P212121 model captures the structure in its completeness, 
since the next stretch of DNA and 3 proteins can be reproduced by the ASU in 
that space group (even though I’m fully aware that in theory this ASU should be 
bigger to accommodate the 60 bases long DNA). I’ll think about it some more..

Best wishes,
Ronnie

--
Ronnie Berntsson, PhD
Chair of the Young Academy of Sweden

Department of Medical Biochemistry and Biophysics, Umeå University
90187 Umeå, Sweden
e-mail: ronnie.bernts...@umu.se
phone: +46 90 7865235
web: https://www.biostruct.umu.se/principal-investigators/ronnie-berntsson/

From: Phil Jeffrey 
Date: Monday, 31 July 2023 at 17:10
To: Ronnie Berntsson 
Subject: Re: [ccp4bb] Connecting DNA between asymmetric units?
Hi Ronnie

Well, technically, your asymmetric unit is only an approximation, since
your true asymmetric unit would hold one entire DNA duplex.  One could
argue that you've misindexed, you've got pseudo-centering, and you
should test a 4x/16x/64x larger cell to see if you can see the ends of
the DNA.

You should go back to the original diffraction images and see if there
are any non-integrated spots between the indexed spots with your
current/smaller cell.  If there are, this might be a priori experimental
evidence that your true cell is larger than your indexed cell.  These
spots might be weak (because your smaller/current unit cell is an ok
approximation) but if they are there then you should treat the cell
differently.

If they're not there, then your DNA is disordered in the formal sense,
and you should probably come up with a model that encapsulates that
disorder with multiple DNA sequences overlapping in space, which then
shows up in the PDB file.  If your 60 bp DNA folds into 4 (?) asymmetric
units, even without bending, I've got to thing that there is evidence of
multi-conformation visible somewhere, which you should then model.
You'll still need some explanatory text in the header - there's no
single model in the smaller unit cell that can convey what you think is
going on in this case.

Cheers
Phil
Princeton




On 7/31/23 10:12 AM, Ronnie Berntsson wrote:
> Hi all,
>
> We have recently solved a structure of a DNA binding protein in complex
> with DNA to ca 2.5 Å. The space group is P212121 and contains 3 protein
> molecules in the asymmetric unit (current Rwork/Rfree = 20.4/24.1). The
> protein was crystallized together with a 60 bases long poly-A oligo
> (ssDNA). Each protein molecule binds to a stretch of this DNA. However,
> only 15 bp of the DNA is part of the asymmetric unit, with each protein
> molecule binding 5 bp. The DNA then goes on to the next ASU (with its 3
> proteins) and so forth. There is no sequence specificity to the DNA, so
> it can “slide”. Redoing the structure in P1 does not really help, as due
> to its “sliding” nature the density is still continuous in between ASUs.
>
> Currently, the structure model thus consists of 3 protein molecules and
> one 15 bases long DNA. However, the density for the DNA is as I wrote
> continuous into the neighboring ASUs. Any advice for how to deal with
> this in the model would be most welcome! We can of course explain it in
> the manuscript that we’ll submit, but would feel good if one can
> represent it in a better way also in the pdb. Hopefully I’ve managed to
> convey my question here, but let me know if any clarification is needed.
>
> Best wishes,
>
> Ronnie
>
> --
> Ronnie Berntsson, PhD
> Chair of the Young Academy of Sweden
>
> Department of Medical Biochemistry and Biophysics, Umeå University
> 90187 Umeå, Sweden
> e-mail: ronnie.bernts...@umu.se 
> phone: +46 90 7865235 
> web:
> https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.biostruct.umu.se%2Fprincipal-investigators%2Fronnie-berntsson%2F=05%7C01%7Cronnie.berntsson%40UMU.SE%7C612e0f61b51a473de7d208db91d83bad%7C5a4ba6f9f5314f329467398f19e69de4%7C0%7C0%7C638264130285558994%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=ekyQiaQOJIEGJvF%2Bcn8SpqPLxpYU9Xsr3pqVtRdKNMY%3D=0
> 

[ccp4bb] CoSeC Conference 2023 | Call for Presentations

[Martyn Winn - STFC UKRI]

Dear All,

Please see below an announcement from our umbrella organisation CoSeC. This is 
an annual meeting with a wider scope of computational science.

Cheers
Martyn


Computational Science Centre for Research Communities (CoSeC) 2023 Conference 
6th of December 2023
Call for Presentations - Deadline 31st October 2023
Further details -  call for presentations for speakers at the 2023 CoSeC 
Conference

The Computational Science Centre for Research Communities (CoSeC) invites 
submissions for its next annual conference, to be held at the Manchester Centre 
Convention Complex on Wednesday the 6th of December 2023 in conjunction with 
the Computing Insight UK event.

This is an opportunity for those involved in activities supported by CoSeC 
(Collaborative Computational Projects, High-End Consortia, and other activities 
within the UKRI Digital Research Infrastructure landscape) to present 
cross-cutting aspects of their work to like-minded researchers as well as 
leading members of the computing industry.

We invite abstract submissions around the following topics:


* Modelling, Simulation & Reconstruction: All aspects of computational 
science related to modelling, simulation and reconstruction. It is important 
that presented work be of interest to those outside of its immediate scientific 
community, with the most relevant work being that which has potential 
applications across the sciences.


* Scientific Reproducibility: Work relating to enabling reproducibility 
across computational science, from workflows through to ensuring data is 
produced and stored in accordance with the principles of FAIR (findable, 
accessible, interoperable, reproducible).


* Applied Artificial Intelligence and Machine Learning: The use or 
development of AI or ML data science approaches within the context of 
computational science. The most relevant work is likely to provide clear 
application beyond the fundamental and have potential applications across the 
sciences.


* Large Scale Computing for Computational Science: All aspects are 
invited for submission, from applied supercomputing (e.g. developments toward 
exascale and work related to the use of national infrastructure like ARCHER2) 
through to topics around accessibility, and usability of computational science 
methods or software on large scale computing platforms.

Accepted speakers will be able to present their work in Manchester with no 
associated registration fees as well as gain access to the full CIUK event on 
the 7th and 8th of December. Upon acceptance an optional extended version of 
the abstract will be published as part of the main CIUK conference proceedings.

For more details about CoSeC, the work we do and communities we support, please 
refer to our webpage: https://cosec.stfc.ac.uk/.

Contact CoSeC: co...@stfc.ac.uk



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