[ccp4bb] PhD student position in physiological temperature crystallography

[Marcus Fischer]

*PhD student position*



The Fischer lab at St. Jude Children’s Research Hospital is recruiting a
graduate student for a structural biology project that exploits protein
dynamics for ligand discovery against pediatric cancer targets.



*Our lab specializes in crystallography at physiological temperatures to
reveal hidden insights into the protein conformational landscape that is
relevant for function and ligand discovery.*



You will be part of an interdisciplinary team that uses structural biology,
biochemistry, biophysics and computation to characterize dynamic,
disease-relevant states of proteins, ligands and water networks. By finding
ligands against those flexible protein states, and revealing allosteric
networks we can explore new ways to modulate protein malfunction in disease.



This work will provide a solid training in current opportunities within
structure-based ligand discovery with relevance for both academia and
industry.  The project is housed in the Department of Chemical Biology and
Therapeutics
,
and Structural Biology

 at St. Jude Children’s Research Hospital. It builds on strong investments
into a world-class infrastructure in structural and chemical biology. With
its excellent core facilities, highly interactive and supportive
environment, St. Jude Children’s Research Hospital is a great place to do
research and build a career whilst living in an affordable city.



Accompanying courses will be taken in conjunction with the Department of
Pharmaceutical Sciences at the University of Tennessee Health Science
Center.



Admission requirements:

-   a BS or MS degree in physics, chemistry, biology, mathematics,
engineering, or other appropriate disciplines.

-   a minimum Grade Point Average of 3.0

-   a combined Graduate Record Examination score (verbal and
quantitative) of at least 300

-   proof of proficiency in English (e.g. TOEFL)



Optional qualifications:

-   Hands-on molecular biology and crystallography experience



Please direct your questions and application package including a current CV
and cover letter that describes your interest and relevant qualifications
to: Dr. Marcus Fischer (marcus.fisc...@stjude.org) by February 21st 2022.



Online application deadline is March 15th for admission to the Fall
Semester starting in August 2022.



*Relevant papers include:*

• Bradford et al. (2021). Temperature artifacts in protein structures bias
ligand-binding predictions. *Chemical Science*. DOI: 10.1039/D1SC02751D

• Fischer (2021). Macromolecular room temperature crystallography. *Q Rev
Biophys* 54. E1

• Darby et al. (2019). Water Networks Can Determine the Affinity of Ligand
Binding to Proteins. *JACS* 141, 15818-26.

• Balius et al. (2017). Testing inhomogeneous solvation theory in
structure-based ligand discovery. *PNAS* E6839-46.

• Fischer et al. (2015). One crystal, two temperatures: cryocooling
penalties alter ligand binding to transient protein sites. *Chembiochem*
1560-64.

• Fischer et al. (2014). Incorporation of protein flexibility &
conformational energy penalties in docking screens to improve ligand
discovery. *Nature Chemistry* 6, 575-83.



More info at: https://www.stjude.org/fischer



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[ccp4bb] Baculovirus expression system

[Srivastava, Dhiraj]

Thank you every one for all your input. Our concern was whether there is any 
new advanced system than Bac-to-Bac or Bac-to-Bac is still pretty standard 
system for baculovirus expression. Based on all your inputs, it appears that we 
are not very outdated in our information about baculovirus expression system. 
There may be few newer systems but not much advanced than Bac-to-Bac and don't 
save significant amount of time and effort.

Thank you
Dhiraj



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[ccp4bb] LINXS Integrative Structural Biology Symposium, May 4-6, 2022, Lund, Sweden

[Thomas Ursby]

Dear all,

LINXS 3rd Integrative Structural Biology symposium will take place in 
Lund, Sweden, May 4-6, 2022.


Please check out the web site for more information:

https://www.linxs.se/events/2022/5/4/linxs-3rd-integrative-structural-biology-symposium-may-4-6-in-lund

or the Indico page:

https://indico.linxs.lu.se/event/268/

Best regards,
Thomas

LINXS - Lund Institute of advanced Neutron and X-ray Science
https://www.linxs.se/



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Re: [ccp4bb] Thanks

[Jon Agirre]

Thank you Clare for all your contributions to the community throughout
these 25 years, particularly for bringing the technicians' perspective into
focus, and providing helpful feedback. You will be missed.
Best of luck in your next role,
Jon

On Wed, 9 Feb 2022 at 09:58, Clare Stevenson (JIC) <
clare.steven...@jic.ac.uk> wrote:

> I have subscribed to the CCP4 bulletin board for over 25 years and
> attended many CCP4 meetings. I am changing role shortly and will no longer
> be a crystallographer so will unsubscribe from the board. I just wanted to
> pass on my thanks to everyone who has written posts, contributed to
> discussions and answered questions. It always amazes me just how great the
> crystallography CCP4 community is and it has been great to be involved in
> it.
>
>
>
> Have fun
>
>
>
> Clare
>
>
>
>
>
> Dr Clare E.M. Stevenson
>
> John Innes Centre
>
> Norwich Research Park
>
> Colney Lane
>
> Norwich
>
> NR4 7UH
>
> Tel 01603 450734
>
>
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>


-- 
Dr Jon Agirre
Royal Society Olga Kennard Research Fellow
CCP4 ED champion | Instruct representative @ 3D-Bioinfo (Elixir)
York Structural Biology Laboratory, Department of Chemistry
University of York, Heslington, YO10 5DD, York, UK
http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/
Office: /B/K/065 Phone: +44 (0) 1904 32 8252
Twitter: @glycojones



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Re: [ccp4bb] Updating Ubuntu 18 LTS to 20?

[Kay Diederichs]

I have updated Ubuntu on notebooks a couple of times from one LTS release to 
the next. This works well (and is tested) for those packages that are part of 
the old release, but it does not necessarily work well for packages outside the 
distribution.
apt-mark showmanual
should show those manually installed packages on Ubuntu.

(With Arch Linux or Manjaro you can use 
pacman -Qe 
instead. In case of Fedora, 
dnf history userinstalled 
should produce a list. In CentOS 7,
yum history addon-info
may be a start.)

Obviously you'll have to keep an eye on those extra packages. They will not 
necessarily be upgraded, and they may even prevent the upgrade from one LTS to 
the next. 
When taking this into account, upgrades of LTS versions have worked for me.

Hope this helps,
Kay



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[ccp4bb] Thanks

[Clare Stevenson (JIC)]

I have subscribed to the CCP4 bulletin board for over 25 years and attended 
many CCP4 meetings. I am changing role shortly and will no longer be a 
crystallographer so will unsubscribe from the board. I just wanted to pass on 
my thanks to everyone who has written posts, contributed to discussions and 
answered questions. It always amazes me just how great the crystallography CCP4 
community is and it has been great to be involved in it.

Have fun

Clare


Dr Clare E.M. Stevenson
John Innes Centre
Norwich Research Park
Colney Lane
Norwich
NR4 7UH
Tel 01603 450734




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