[ccp4bb] Structural Biology Scientist position at Foghorn Therapeutics in Cambridge, MA

2018-02-16 Thread Jeremy Setser 
Foghorn Therapeutics has a job opportunity for an early career PhD in 
Structural Biology. Please apply directly to the official posting:

http://foghorntherapeutics.applytojob.com/apply/nkSaJJ1Rrn/Scientist-Structural-Biology?referrer=20180209182508A5FGUVSWUYZTBVFU=email

POSITION SUMMARY
TITLE:  Scientist, Structural Biology
REPORTS TO: Senior Scientist, Drug Discovery
LOCATION:Cambridge, MA
COMPANY DESCRIPTION
Founded in 2016, Foghorn Therapeutics discovers and develops novel drugs to 
treat cancer and other serious medical disorders. The company seeks to discover 
novel therapeutics that target chromatin remodeling complexes. Foghorn uses a 
proprietary platform based on revolutionary advances in mechanistic 
understanding of disease.
POSITION DESCRIPTION
We are seeking a highly skilled and motivated structural biologist to become an 
integral member of the Foghorn team. This person will contribute to our goal of 
developing transformative therapeutics by planning and carrying out structural 
characterization of crucial drug targets. The main focus of this role will be 
protein crystallography but will require a willingness to find new ways to 
think about scientific challenges. We need someone who is passionate, driven, 
and ambitious to help us achieve our goal of improving patients’ lives.
Responsibilities include:

  *   Collaborating with colleagues in biochemistry, biology, and chemistry to 
develop structural biology strategy.
  *   Designing biophysics-grade protein constructs and assisting in the 
optimization of purification protocols.
  *   Crystallization, X-ray structure determination, and analysis of important 
drug targets.
  *   Providing regular updates to cross-functional teams and helping guide 
structure-based compound design in close collaboration with chemistry group.
  *   Participating in the management of collaborations with contract research 
organizations (CROs) and academic partners.
QUALIFICATIONS

  *   PhD in Structural Biology, Biophysics, Biochemistry or a closely related 
field, with a background in chemistry.
  *   Demonstrated competency in protein construct design and expression and 
purification strategies using bacterial, insect, and mammalian hosts. 
Experience with multi-protein complexes is a plus.
  *   Deep expertise in protein crystallization and X-ray structure 
determination of protein-ligand complexes.
  *   Extensive knowledge of protein structure and function, with the ability 
to articulately communicate structural information to a broad audience.
  *   Experience with other structural techniques (e.g. electron microscopy, 
small-angle X-ray scattering) is preferred.
  *   Excellent time management and communication skills.
  *   Ability to work in a fast-paced, team-driven environment, with a 
collaborative and proactive attitude.
- - - - - - - - - - - - - - - - - - - - - - - -
Jeremy W. Setser, PhD
Senior Scientist, Drug Discovery
Foghorn Therapeutics
jset...@foghorntx.com

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[ccp4bb] Vacancy for scientific data curator (EMDB/EMPIAR) at EMBL-EBI

2018-02-16 Thread Ardan Patwardhan 
Dear all

We are looking to recruit an expert structural biologist with cryo-EM 
experience as a Scientific Data Curator for EMDB and EMPIAR. 

The post holder will work with the annotation and biocuration of the EMDB and 
EMPIAR archives. The biocuration activity with also involve improving the 
integration of EMDB and EMPIAR data with other bioinformatics resources. In 
order to make resources more accessible to a wide spectrum of biomedical users 
the post holder will also help with user-experience (UX) testing, outreach and 
training.

For more information, please go to:

https://www.embl.de/jobs/searchjobs/index.php?ref=EBI_01149=1 



Feel free to pass the information on to any potentially interested and 
qualified people you may know.

Many thanks and best wishes

Ardan Patwardhan
Team Leader - Cellular Structure & 3D Bioimaging
EMDB & EMPIAR
European Bioinformatics Institute (EMBL-EBI) European Molecular Biology 
Laboratory
Wellcome Genome Campus
Hinxton, Cambridge CB10 1SD
Tel: +44 1223 492649

[ccp4bb] Post doctoral position in structure-based hit discovery for antibiotic targets (Bergen, Norway)

2018-02-16 Thread Ruth Brenk 

Hi,

just a reminder that I have an open position in my group at the 
University of Bergen (Norway) for structure-based hit discovery for 
targets for antibiotics.


The deadline for applications is this Sunday.

I am looking for somebody with experience in at least one of the 
following areas:


X-ray crystallography of macromolecules
Assay development using surface plasmon resonance (SPR) or biolayer 
interferometry (BLI)

Fragment screening

Additional experience in any of the following fields will be an advantage:

structure-based ligand design using computational methods
recombinant protein expression and purification
diffraction data collection at synchrotron beamlines

https://www.jobbnorge.no/en/available-jobs/job/147097/postdoctoral-fellow-3-years-in-structure-based-hit-discovery-for-antibiotics

You are welcome to contact me for more information but the application 
has to be send via jobbnorge.no.


Regards

Ruth

--
Prof. Dr. Ruth Brenk
University of Bergen
Department of Biomedicine

ruth.br...@uib.no
+47 55586070

Visitor adress:  Mail address:
Jonas Lies vei 91Postboks 7804
5020 Bergen  5020 Bergen
Norway   Norway

[ccp4bb] PhD Position: Structural Mechanisms of Ubiquitination Enzymes in Disease

2018-02-16 Thread Sonja Lorenz 

PhD Position
Structural Mechanisms of Ubiquitination Enzymes in Disease

We invite applications for a PhD position in the research group of Dr.  
Sonja Lorenz at the Rudolf Virchow Center for Experimental  
Biomedicine, Würzburg, Germany.
The successful applicant will have the opportunity to enroll in the  
‘Graduate School of Life Sciences’ in Würzburg – a prestigious  
international PhD program funded by the German Excellence Initiative.


The Lorenz lab is supported by the Emmy Noether Program of the German  
Research Foundation and the EMBO Young Investigator Program among  
other sources. We aim to uncover the catalytic and regulatory  
mechanisms of ubiquitination enzymes and their functions in cancer and  
infection. Our lab combines structural biology (X-ray crystallography,  
NMR spectroscopy, cryo-EM) with biochemical and cell biological  
analyses.


The Rudolf Virchow Center is a highly competitive international  
research institute with an outstanding technical infrastructure. The  
Lorenz lab has access to state-of-the-art instrumentation in X-ray  
crystallography, high-field NMR, cryo-EM, and an extensive range of  
modern biophysical and cell biological equipment. We are integrated  
into a stimulating research environment that includes the Biocenter,  
the Institute for Molecular Infection Biology, the Helmholtz Institute  
for RNA-Based Infection Research, the Max Planck Research Group for  
Systems Immunology, and the University Hospital in Würzburg.


Applicants should have a M.Sc. or comparable degree in in molecular  
biology, biochemistry or a related discipline and a strong interest in  
structure-function studies on proteins. Experience in protein  
biochemistry and biophysical techniques is desirable. Good English  
language skills are essential; knowledge of German is not required.


The position can start immediately or upon mutual agreement. Salary  
will be according to the German TVL scale. In case of equivalent  
qualifications, disabled applicants will be preferentially considered.  
Würzburg is located in the beautiful, wine-growing area of Franconia  
and in proximity to Frankfurt (1 hour by train) and Munich (2 hours by  
train).


Applications should be sent to Sonja Lorenz by email  
(sonja.lor...@virchow.uni-wuerzburg.de) and are expected to include a  
letter of motivation detailing research interests and expertise, a CV,  
and the contact information for at least two references. Review of  
applications will begin immediately.



http://www.virchow.uni-wuerzburg.de/lab_pages/slorenz

http://www.rudolf-virchow-zentrum.de/en/research/research-groups/lorenz-group/research.html

Sonja Lorenz, PhD
Rudolf Virchow Center for Experimental Biomedicine
Josef-Schneider-Strasse 2, Haus D15
97080 Würzburg, Germany

Re: [ccp4bb] protein quasicrystals?

2018-02-16 Thread Harry Powell 
Just to add to the list, Mosflm can handle multiple crystals without prior 
knowledge and is distributed as part of  CCP4 

Harry
--
Dr Harry Powell
Chairman of European Crystallographic Association SIG9 (Crystallographic 
Computing) 




On 15 Feb 2018, at 22:03, Richard Staples wrote:

> I agree with Joe CrysAlisPro works very well.
>  
>  
>  
> Dr. Richard J. Staples
> Crystallographer
> Department of Chemistry
> 578 S. Shaw Lane
> Michigan State University
> East Lansing, MI 48824
> stap...@chemistry.msu.edu
> 517-353-1074
> Lab: 517-353-1079
>  
>  
>  
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of Joseph 
> Ferrara
> Sent: Thursday, February 15, 2018 4:57 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] protein quasicrystals?
>  
> Nakane-san,
>  
> There is also CrysAlisPro, which can handle multiple crystals and may already 
> support your detector. If you send me the data, offline, I would be happy to 
> pass it onto the CrysAlisPro development team for testing.
>  
> Joseph D. Ferrara, Ph.D.
> CSO
> Deputy Director, X-ray Research Laboratory
> Vice President, American Crystallographic Association
>  
> Rigaku Corporation
> 9009 New Trails Drive
> The Woodlands, TX 77381
> Tel: 281-362-2300 x 168
> Skype: xrayjoe
> url: www.rigaku.com
>  
>  
>  
> From: CCP4 bulletin board [mailto:CCP4BB@JISCMAIL.AC.UK] On Behalf Of James 
> Phillips
> Sent: Tuesday, February 13, 2018 2:03 PM
> To: CCP4BB@JISCMAIL.AC.UK
> Subject: Re: [ccp4bb] protein quasicrystals?
>  
> There are programs which are good at indexing patterns from multiply twinned 
> crystals. Bruker AXS has one, to my knowledge. There may be other sources. I 
> suggest you try that first before you invoke a quasicrystal explanation.
>  
>  
>  
>  
> James Phillips
>  
> On Tue, Feb 13, 2018 at 12:07 PM, Takanori Nakane  
> wrote:
> Hi,
> 
> "dials.reciprocal_space_viewer" is very useful to identify multiple lattices.
> For quasicrystal and modulated crystals, "dials.rs_mapper" is also very
> useful.
> 
> Best regards,
> 
> Takanori Nakane
> 
> > Have you tried microseeding of these sphere crystals? It may help to get
> > better crystals.
> >
> >
> > Burak
> >
> > 
> > From: CCP4 bulletin board  on behalf of Yu Qiu
> > 
> > Sent: 13 February 2018 15:09:43
> > To: CCP4BB@JISCMAIL.AC.UK
> > Subject: [ccp4bb] protein quasicrystals?
> >
> >
> > Hi,
> >
> >
> >
> > I have been trying to crystallize a protein complex and keep getting
> > sphere shape crystals. The diffraction is around 3 angstrom, but looks
> > like multiple lattices. I am wondering if it could be a quasi crystal? Is
> > there anyone has such experience?
> >
> >
> >
> > Thanks,
> >
> > Yu
> >
>

Re: [ccp4bb] 3D Structure Search

2018-02-16 Thread Briggs, David C 
Also,


TopSearch https://topsearch.services.came.sbg.ac.at/

CAME - TopSearch :: Structure Search
topsearch.services.came.sbg.ac.at
Sequence Analysis Highlight identical residues Jmol Mode HTML5 Java. Cite 
TopSearch ©

Dave


==

Dr David C Briggs

Hohenester Lab

Department of Life Sciences

Imperial College London

UK

http://about.me/david_briggs


From: CCP4 bulletin board  on behalf of Daniel Rigden 

Sent: 16 February 2018 08:29:29
To: CCP4BB@JISCMAIL.AC.UK
Subject: Re: [ccp4bb] 3D Structure Search

Another topology-independent method is CLICK, available as a server here

http://cospi.iiserpune.ac.in/click/

You might also want to try FATCAT which considers potential flexibility
of separate subdomains in its structural alignment

http://fatcat.burnham.org/fatcat-cgi/cgi/fatcat.pl?-func=search

Dan


On 15/02/18 23:25, Ethan A Merritt wrote:
> On Thursday, February 15, 2018 3:16:50 PM PST Nicola Evans wrote:
>> I have recently solved a novel structure which previously did not have any 
>> structural homologues (as related by sequence identity). I was wondering if 
>> anyone could recommend a 3D structural search engine? I used the Dali server 
>> which has been recommended to me in the past (and with past success) but the 
>> top few hits this time aren't similar structurally (although I haven't 
>> exhausted the list yet). I just want to confirm if the folds are truly novel 
>> or not.
> Dali is sensitive to the order of secondary structure elements.
> This is relevant if you are looking for evolutionary relatedness, but
> not if you just want to ask "does it look like this".
>
> For the latter question, I suggest the VAST server at NCBI.
> https://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml
>
>Ethan
>

--
Dr Daniel John Rigden Tel:(+44) 151 795 4467
Institute of Integrative Biology  FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool   http://pcwww.liverpool.ac.uk/~drigden/
Crown St.,
Liverpool L69 7ZB, U.K.

Re: [ccp4bb] 3D Structure Search

2018-02-16 Thread Daniel Rigden 

Another topology-independent method is CLICK, available as a server here

http://cospi.iiserpune.ac.in/click/

You might also want to try FATCAT which considers potential flexibility 
of separate subdomains in its structural alignment


http://fatcat.burnham.org/fatcat-cgi/cgi/fatcat.pl?-func=search

Dan


On 15/02/18 23:25, Ethan A Merritt wrote:

On Thursday, February 15, 2018 3:16:50 PM PST Nicola Evans wrote:

I have recently solved a novel structure which previously did not have any 
structural homologues (as related by sequence identity). I was wondering if 
anyone could recommend a 3D structural search engine? I used the Dali server 
which has been recommended to me in the past (and with past success) but the 
top few hits this time aren't similar structurally (although I haven't 
exhausted the list yet). I just want to confirm if the folds are truly novel or 
not.

Dali is sensitive to the order of secondary structure elements.
This is relevant if you are looking for evolutionary relatedness, but
not if you just want to ask "does it look like this".

For the latter question, I suggest the VAST server at NCBI.
https://www.ncbi.nlm.nih.gov/Structure/VAST/vast.shtml

Ethan



--
Dr Daniel John Rigden Tel:(+44) 151 795 4467
Institute of Integrative Biology  FAX:(+44) 151 795 4406
Room 101, Biosciences Building
University of Liverpool   http://pcwww.liverpool.ac.uk/~drigden/
Crown St.,
Liverpool L69 7ZB, U.K.