[ccp4bb] Postdoctoral position available at the Institute of Cancer Research, London UK

[Rob Van Montfort]

The Institute of Cancer Research (ICR), London, is one of the world’s most 
influential cancer research institutes, with an outstanding record of 
achievement dating back more than 100 years. Under the leadership of our Chief 
Executive, Professor Paul Workman FMedSci, the ICR is ranked as the UK’s 
leading academic research centre. Together with our partner The Royal Marsden 
Hospital, we are rated in the top four cancer centres globally. The ICR is 
committed to attracting, developing and retaining the best minds in the world 
to join us in our mission – to make the discoveries that defeat cancer.


The Cancer Research UK Cancer Therapeutics Unit (CTU), within the Division of 
Cancer Therapeutics, is a multidisciplinary 'bench to bedside' centre, 
comprising around 160 staff dedicated to the discovery and development of novel 
therapeutics for the treatment of cancer. The CTU’s exciting goal is to 
discover high quality small molecule drug candidates and to progress these to 
clinical trial. All the scientific disciplines are in place to make this 
possible, including medicinal chemistry, biology, structural biology, assay 
scientists, drug metabolism and clinical specialists.

A postdoctoral position is available in Dr Rob van Montfort’s Hit Discovery and 
Structural Design Team within the CTU in Sutton. The Post-doc will be involved 
in the structure determination of protein complexes by cryo-electron microscopy 
(cryoEM) as part of CTU research programmes in targeted protein degradation. 
The postholder will be responsible for sample preparation, structure 
determination by cryoEM, and subsequent structural analysis of protein 
complexes and will interact closely with the structural biologists and biology, 
computational chemistry and medicinal chemistry teams at the CTU. The 
successful candidate will also be part of the Division of Structural Biology, 
located in Chelsea, in which the structural biologists in Dr van Montfort’s 
team are embedded, and will have access to its state-of-the art cryoEM 
facilities. These include an in-house Glacios and 30% direct access to a Titan 
KRIOS located at the Francis Crick Institute. Both microscopes are equipped 
with Falcon III detectors and volta phase plates (VPP). In addition, we have 
excellent access to the electron bioimaging Centre (eBIC) at the Harwell 
Science and Innovation campus, Didcot, UK. The postholder will be expected to 
work across the two sites in Chelsea, London and Sutton, Surrey.

Applicants must have a PhD (or equivalent) in a biological or physical science, 
with experience in cryo-EM specimen preparation and data processing. Experience 
in single particle electron microscopy is essential for this post. Experience 
in molecular biology and protein expression in insect cells will be an 
advantage.

The starting salary for the position will be in the range £32,844 to £40,902 
p.a. inclusive (based on previous post-doctoral experience) and the post is 
offered on a fixed term contract of 18 months. Informal enquiries to 
rob.vanmontf...@icr.ac.uk or 
yann-vai.lebi...@icr.ac.uk.
Please DO NOT send your application to Dr van Montfort or Dr Le Bihan, but 
apply via the e-recruitment system on our website 
www.icr.ac.uk.


Closing date:  21st February 2021


Dr. Rob van Montfort
Reader in Structural Biology and Cancer Drug Discovery
Team Leader Hit Discovery and Structural Design
Divisions of Cancer Therapeutics and Structural Biology
The Institute of Cancer Research
15 Cotswold Road
Sutton SM2 5NG
UK

Tel:
+44-(0)20-8722-4364 (Sutton)
+44-(0)20-7153-5142 (Chelsea)
Email: rob.vanmontf...@icr.ac.uk


The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

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[ccp4bb] AbbVie industrial postdoc position available

[Nocek, Boguslaw P]

Hello Everyone,
A postdoctoral position is available immediately in the Cystic Fibrosis Group 
led by Dr. Ashvani Singh at AbbVie Inc,  in Illinois, USA.  Successful 
candidate will work with a cross-functional team of researchers to Investigate 
the Structure-Function Relationship of CFTR Using CFTR Modulators and 
Understand their Clinical Translation.
Qualified candidate should have a PhD in Biochemistry 
(Biochemistry/Pharmacology/Cell and Molecular Sciences/Structural Biology) with 
no more than 3 years of prior postdoctoral experience. Experience in membrane 
protein expression, purification and biochemistry is required and a strong 
background in CFTR pharmacology is preferred.  Key responsibilities include 
expression and purification of disease mutants and biochemical, biophysical, 
and structural studies.  Previous experience in Cryo-EM is preferred but not 
essential. Selected candidate will have the opportunity to learn Cryo-EM.

For more information and to apply online, please visit:

https://careers.abbvie.com/jobs/2007216?lang=en-us#.X48n8qJQthg.mailto

Req ID: 2100410




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[ccp4bb] Subscribe

[Sridhar Prasad]

*G. Sridhar Prasad, PhD*
*Chief Scientific Officer*

*Plex Pharmaceuticals & Collidion Inc.*
*6330 Nancy Ridge Drive, S105**San Diego, CA 92121*

*Ph: 858-587-8800 (o)**858-733-0858 (M)*
*spra...@plexpharma.com *
*www.plexpharma.com *

*www.collidion.com *

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advised that any dissemination, distribution, or use of the contents of
this message is strictly prohibited. If you received this e-mail message in
error, please e-mail i...@plexpharma.com and contact the sender by reply
e-mail. Please also permanently delete all copies of the original e-mail
and any attached documentation. Thank you.



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Re: [ccp4bb] Help for Twin Refinement in Refmac5 / CCP4i2

[Eleanor Dodson]

I fell into the same trap this week. Apparently if in the first screen you
tick the box Crystal is twinned” the interface resets the input data to
FMEAN (or IMEAN if you have asked to use intensitirs) and you don’t need to
say TWIN .
Semi logical I guess but easy to miss. Eleanor

On Tue, 26 Jan 2021 at 06:42, Parthasarathy Sampathkumar 
wrote:

> Dear All,
>
> Please you may ignore my previous email. TWIN refinement in Refmac5 /
> CCP4i2 worked well once used "HKLOUT_0-observed_data_asIMEAN.mtz" from
> the data-reduction job. I am slowly getting used to the finer-aspects of
> CCP4i2. Previously, I used to have both Intensities and Amplitudes in a
> single MTZ file :-)
>
> Thanks,
> Partha
>
> On Mon, Jan 25, 2021 at 9:47 PM Parthasarathy Sampathkumar <
> spart...@gmail.com> wrote:
>
>> Dear All,
>>
>> I have not had much experience in refining structure using data from
>> twinned crystals and has started using CCP4i2 very recently only.
>>
>> Here is a background:
>> antigen-Fab crystal structure determined by MR first in P4(3)2(1)2 space
>> group with 1-complex molecule in the asymmetric unit (ASU). Later, I
>> reprocessed the data in P4(3) performed MR to search for the 2nd molecule
>> and refined the structure using Refmac5 without the "twin" keyword. With
>> the sequence fully modeled for the two complex molecules in the ASU current
>> Rcryst = 27.8%and Rfree = 33.2%. Unit cell = "59.9, 59.9, 404.5, 90.0,
>> 90.0, 90.0".
>>
>> Twin fraction estimates from Britton plot = 0.47 and from H-test = 0.43,
>> as reported by AIMLESS. Then, attempted TWIN refinement in Refmac5 /
>> CCP4i2 by adding the keyword "twin" in the advanced options. However,
>> getting following error in the log-file:
>>
>>  Error==> array size in mtz_refl_read_int
>> 
>>  Refmac:  Problem with array sizes
>>
>> Does Refmac5 expects intensities here?!!
>> Any help is greatly appreciated.
>>
>> Best Wishes,
>> Partha
>>
>>
>>
>>
>>
> --
>
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[ccp4bb] Imaging system

[Linnert, Dr. Miriam]

Dear all,

We are looking to purchase a new imaging & plate storage system for protein 
crystallization. I would be interested to know what other people use and what 
their personal opinion (experience) of the available options is.

Please feel free to contact me directly.

Thanks in advance,
Miriam

__
Dr. Miriam Linnert
Research Associate
Fraunhofer Institute for Cell Therapy and Immunology IZI
Department of Drug Design and Target Validation MWT
Biocenter, Weinbergweg 22, 06120 Halle (Saale), Germany
miriam.linn...@izi.fraunhofer.de





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[ccp4bb] Postdoctoral position at ICTER in Warsaw, Poland

[Humberto Fernandes]

Dear all 





This is a final reminder for this post. The closing date is the 31st of 
January. 



In the Integrated Structural Biology laboratory at The International Center for 
Translational Eye Research (ICTER) in Warsaw, Poland, one postdoctoral position 
is available for highly motivated biologists, biochemists, or structural 
biologists, for 34 months (maximum planned period of contract: 31/12/2023). The 
position involves cloning, protein production, purification, characterization, 
and structural elucidation of proteins from the visual cycle. 



For details, and how to apply until 31st January, see: 

[ https://ichf.edu.pl/en/job/mcbo-33-2021 | 
https://ichf.edu.pl/en/job/mcbo-33-2021 ] 



Feel free to spread this information at your institutes and to interested 
colleagues. And please do not hesitate to contact me if you have any questions. 
To apply, please send the requested documents to [ 
mailto:icter_j...@ichf.edu.pl | icter_j...@ichf.edu.pl ] . 



Thank you and have a great day, 

Humberto 



[ http://www.icter.pl/ | www.icter.pl ] 

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Re: [ccp4bb] Characterising potential drug-binding pockets

[Barone, Matthias]

Hi Sergei

I assume that you used the term "drug-like fragments" because you would like to 
sort out candidates? The paper referenced by Bernhard is a good way to go, but 
it reflects exactly the problem of PPIs, namely that proteins with well defined 
binding pockets for substrates (such as kinases) are easily recognized while 
the algorithm has problems finding pockets of other PPIs.

I get the feeling that a more directed approach is to test the fragments in 
vitro rather than by simulation. The thought behind is to select for fragments 
that show measurable effects with fast and material-saving methods rather than 
focusing on putative pockets that might or not be recognized by your fragments.

A good example of such a work-flow is https://pubmed.ncbi.nlm.nih.gov/23344974/

best, matthias

[https://cdn.ncbi.nlm.nih.gov/pubmed/persistent/pubmed-meta-image.png]

Using a fragment-based approach to target protein-protein interactions - 
PubMed
pubmed.ncbi.nlm.nih.gov
The ability to identify inhibitors of protein-protein interactions represents a 
major challenge in modern drug discovery and in the development of tools for 
chemical biology. In recent years, fragment-based approaches have emerged as a 
new methodology in drug discovery; however, few examples of smal …




Dr. Matthias Barone

AG Kuehne, Rational Drug Design

Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP)
Robert-Rössle-Strasse 10
13125 Berlin

Germany
Phone: +49 (0)30 94793-284


From: CCP4 bulletin board  on behalf of Sergei Strelkov 

Sent: Monday, January 25, 2021 8:02:07 PM
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] Characterising potential drug-binding pockets


Dear everyone,


In a drug discovery project where our aim is to interfere with some PPIs, we 
could obtain binding of drug-like fragments in several potentially interesting 
pockets on our target. We would like to make a projection on how promising 
these individual pockets are. One way of doing this is through the Sitemap 
program (Halgren, T. A. Identifying and characterizing binding sites and 
assessing druggability. J. Chem. Inf. Model 49, 377–389 (2009)). Are there 
other tools around to do this? In particular, we would like to have accurate 
numbers for the pocket volume, surface, no. of H-bond donors and acceptors, 
average hydrophobicity, etc etc.


Thank you,

Sergei




Prof. Sergei V. Strelkov Laboratory for Biocrystallography Department of 
Pharmaceutical Sciences, KU Leuven O, Campus Gasthuisberg, Herestraat 49 bus 
822, 3000 Leuven, Belgium Phone: +32 16 33 08 45, mobile: +32 486 29 41 32 Lab 
pages: 
http://pharm.kuleuven.be/Biocrystallography



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