Re: [ccp4bb] cation-aromatic database

[Emilia Arturo]

I have used the CaPTURE tool for several years now to identify potential
cation-pi interactions I might have missed during visual inspection of a
model I'm building or perusing. It now seems that the webserver
is no longer connected to the PDB, so one needs to upload coordinates
rather than input a PDB code, but it still works as of today! I'm not sure
how the tool treated ligands, however.

 http://capture.caltech.edu/

Emily.
Emilia ("Emily") C. Arturo
Postdoctoral research associate
Laboratory of Dr. Erica Ollmann Saphire
Center for Infectious Disease and Vaccine Research
La Jolla Institute for Immunology, California USA
Twitter @moonlighterturo @ljiresearch @EOSpahire




On Tue, Apr 20, 2021 at 1:21 PM Soisson, Stephen M <
338a268c4763-dmarc-requ...@jiscmail.ac.uk> wrote:

> Might anyone be aware of a similar database tracking small molecule
> ligands making cation-pi or pi-cation interactions with proteins?
>
> Cheers,
>
> Steve
>
>
> On Apr 20, 2021, at 3:41 PM, Christine Gee  wrote:
>
> 
>
> *EXTERNAL EMAIL* – Use caution with any links or file attachments.
> Hi Stephan,
>
> It seems to be online at the following
>
> http://cmm.osdd.net/gnsmmg/databases/cad/
>
> Regards
> Christine
>
>
> On Tue, Apr 20, 2021 at 12:27 PM stephen.c...@rc-harwell.ac.uk <
> stephen.c...@rc-harwell.ac.uk> wrote:
>
>> Dear BB,
>>
>> Does anyone know if the cation-aromatic database (Reddy, 2007, Prot Sci)
>> is still available?  The link listed in the manuscript (
>> http://203.199.182.73/gnsmmg/databases/cad/) no longer appears to work.
>>
>> Thanks,
>> Steve
>>
>> Dr Stephen Carr
>> Research Complex at Harwell (RCaH)
>> Rutherford Appleton Laboratory
>> Harwell Oxford
>> Didcot
>> Oxon OX11 0FA
>> United Kingdom
>> Email stephen.c...@rc-harwell.ac.uk
>> tel 01235 567717
>>
>> This email and any attachments may contain confidential, copyrightand or
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>> you are not the intended addressee or an authorized recipient of the
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>> use, copy, retain, distribute or disclose the information in or attached to
>> this email.
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>> necessarily represent those of the Research Complex at Harwell.
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[ccp4bb] PROTAC drug discovery Team Leader at Dundee

[Alessio Ciulli]

Dear all:

we are recruiting a Team Leader to lead a new team of five scientists as part 
of a drug discovery collaboration between my group at the School of Life 
Sciences at the University of Dundee, and Almirall (a global pharmaceutical 
company focused on skin diseases with high level of unmet medical need) and its 
Research Department located in Barcelona, Spain. The successful candidate and 
the team will be based in the new Dundee Centre for Targeted Protein 
Degradation.
https://www.dundee.ac.uk/stories/new-protein-degradation-centre-lead-drug-discovery-revolution
 

We are looking for candidates with outstanding academic or industrial track 
record along with demonstrated ability to lead projects and teams. Relevant 
experience in structural biology and biophysical assays to study protein-ligand 
and protein-protein interactions.  Experience with PROTAC / targeted protein 
degradation drug discovery would be an advantage but is not essential. 

The post is available immediately and for a period of 3 years. Salary will 
depend on experience, but will be up to £49,553. This is a unique opportunity 
to gain experience in industry-style drug discovery within an academic setting.

Apply here:
https://www.jobs.dundee.ac.uk/fe/tpl_uod01.asp?s=4A515F4E5A565B1A=104731,7248764821=149087283=02872369482257=sesuvjpewapqijpwfj

For informal enquiry feel free to reach out to me directly at 
a.ciu...@dundee.ac.uk 


Sent from my iPad


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Re: [ccp4bb] cation-aromatic database

[Soisson, Stephen M]

Might anyone be aware of a similar database tracking small molecule ligands 
making cation-pi or pi-cation interactions with proteins?

Cheers,

Steve


On Apr 20, 2021, at 3:41 PM, Christine Gee  wrote:


EXTERNAL EMAIL – Use caution with any links or file attachments.
Hi Stephan,

It seems to be online at the following

http://cmm.osdd.net/gnsmmg/databases/cad/

Regards
Christine


On Tue, Apr 20, 2021 at 12:27 PM 
stephen.c...@rc-harwell.ac.uk 
mailto:stephen.c...@rc-harwell.ac.uk>> wrote:
Dear BB,

Does anyone know if the cation-aromatic database (Reddy, 2007, Prot Sci) is 
still available?  The link listed in the manuscript 
(http://203.199.182.73/gnsmmg/databases/cad/) no longer appears to work.

Thanks,
Steve

Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717
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Re: [ccp4bb] cation-aromatic database

[Christine Gee]

Hi Stephan,

It seems to be online at the following

http://cmm.osdd.net/gnsmmg/databases/cad/

Regards
Christine


On Tue, Apr 20, 2021 at 12:27 PM stephen.c...@rc-harwell.ac.uk <
stephen.c...@rc-harwell.ac.uk> wrote:

> Dear BB,
>
> Does anyone know if the cation-aromatic database (Reddy, 2007, Prot Sci)
> is still available?  The link listed in the manuscript (
> http://203.199.182.73/gnsmmg/databases/cad/) no longer appears to work.
>
> Thanks,
> Steve
>
> Dr Stephen Carr
> Research Complex at Harwell (RCaH)
> Rutherford Appleton Laboratory
> Harwell Oxford
> Didcot
> Oxon OX11 0FA
> United Kingdom
> Email stephen.c...@rc-harwell.ac.uk
> tel 01235 567717
>
> This email and any attachments may contain confidential, copyrightand or
> privileged material, and are for the use of the intended addressee only. If
> you are not the intended addressee or an authorized recipient of the
> addressee, please notify us of receipt by returning the e-mail and do not
> use, copy, retain, distribute or disclose the information in or attached to
> this email.
>
>
>
> Any views or opinions presented are solely those of the author and do not
> necessarily represent those of the Research Complex at Harwell.
>
>
>
> There is no guarantee that this email or any attachments are free from
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[ccp4bb] cation-aromatic database

[stephen.c...@rc-harwell.ac.uk]

Dear BB,

Does anyone know if the cation-aromatic database (Reddy, 2007, Prot Sci) is 
still available?  The link listed in the manuscript 
(http://203.199.182.73/gnsmmg/databases/cad/) no longer appears to work.

Thanks,
Steve

Dr Stephen Carr
Research Complex at Harwell (RCaH)
Rutherford Appleton Laboratory
Harwell Oxford
Didcot
Oxon OX11 0FA
United Kingdom
Email stephen.c...@rc-harwell.ac.uk
tel 01235 567717

This email and any attachments may contain confidential, copyright and or 
privileged material, and are for the use of the intended addressee only. If you 
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please notify us of receipt by returning the e-mail and do not use, copy, 
retain, distribute or disclose the information in or attached to this email.

Any views or opinions presented are solely those of the author and do not 
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of software viruses which may be transmitted in or with the message.

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[ccp4bb] LINXS Workshop- Structural Resolution of Membrane Proteins: From Expression to Sample Preparation'' , held online on May 25-26, 2021

[Swati Aggarwal]

Dear All,

We want to wish you welcome to the 1st Workshop from LINXS Membrane Protein
Working Group taking place digitally on Zoom. The Membrane Protein Working
Group is dedicated to explore the unique challenges involved in research on
the structural biology of membrane proteins. Our first, "*Structural
Resolution of Membrane Proteins: From Expression to Sample Preparation*''
workshop will focus specifically on three areas: expression systems, sample
preparation and quality control.


*Where:* Online, a zoom link will be provided just before the event
*When:* May 25-26 (noon-to-noon) CET
*Abstract submission deadline:* 5th of May, 2021
*Registration deadline:* 20th May 2021

AIM

The aim is to provide expert overview about different platforms for
recombinant protein productions and purification strategies for
crystallography techniques. Overcoming low yield expression, misfolded
proteins and difficulties in purifying stable functional proteins are among
the most common bottlenecks delaying structural characterization. We invite
scientists to introduce their best practices in these subjects in order to
provide greater knowledge and knowledge transfer on how best to deal with
these challenges.

CONTRIBUTED TALKS

We hope to engage the attendance from PhD students and postdocs from a
range of disciplines, as well as more senior researchers. We are
encouraging participants, and especially PhD students, to consider
presenting their research in a contributed talk (call for abstracts) and
also to promote lively discussions.

CONTENT

*Day 1:*

   - Workshop aims and scope of the general problem
   - Membrane Protein Expression
   - Comparison of different expression systems
   - Success stories vs trouble-shooting problem areas, trial and error


   - Confirmed speakers:
   *Roslyn Bill* (Aston University) - *Recombinant membrane protein
   production in microbial hosts*
   *David Drew* (Stockholm University) - TBA
   *Joseph Lyons *(Aarhus University) - TBA

*Day 2:*

   - Sample Preparation, Quality Control
   - Membrane solubilization and other preparation methods

Confirmed speakers:
*Arjan Snijder* (AstraZeneca) - *Membrane protein purification and
application in drug discovery*
*Christopher G. Tate* (Cambridge University) - *Whipping GPCRs into shape
for structure determination*

In the autumn the plan is to continue further on topics about membrane
protein crystallization techniques, Cryo-EM or neutron structures,
scattering techniques and well-diffracting crystals.

Please find *Registration* and Timetable (will be updated with abstracts)
here: https://indico.linxs.lu.se/event/219/


The LINX organising Team.





Regards,

Swati Aggarwal

Early Stage Researcher

European Spallation Source

Lund, Sweden

email: swati.aggar...@ess.eu



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[ccp4bb] CCP-EM Spring Symposium Starts Today!

[Tom Burnley - STFC UKRI]

Dear all,

A quick reminder that the CCP-EM Spring Symposium starts today.  Full schedule 
is here:

https://www.ccpem.ac.uk/downloads/symposium/ccp-em_symp_schedule_2021.pdf

and registration is free and open here:

https://ukri.zoom.us/webinar/register/WN_p_s9-m73TnK0VYdjWT1stg

All the best,

Tom

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[ccp4bb] PhD student position, Umeå University, Sweden

[Magnus Andersson]

The Andersson lab at the Department of Chemistry at Umeå University, Sweden, is 
looking to recruit a PhD student to join our team to study ATP-dependent 
membrane proteins with a specific focus on regulation mechanisms and bacterial 
antibiotic resistance. We combine structural biology techniques ranging from 
cryo-EM, X-ray solution scattering, and cutting-edge time-resolved X-ray 
scattering to determine structures of high-energy states (see our 2020 
publication in Science Advances) – that are invisible to other structural 
biology techniques. So, if you’re interested in pushing the limits of 
structural biology - come join our team!

Here is a link to the full ad and the application details: 
https://www.nature.com/naturecareers/job/phd-student-position-in-chemistry-umea-university-umu-739108

Best,

Magnus Andersson

#
Magnus Andersson, Associate Professor
Integrated Structural Biology
Department of Chemistry
Umeå University

Email: magnus.p.anders...@umu.se
Phone: +46 720 837370

Mailing address:
Umeå University
Department of Chemistry
KBC-building
SE-901 87 Umeå

Visiting address:
Linnaeusvägen 6




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