[ccp4bb] Homology modeling

2020-08-14 Thread amit gaur 
Hi All,

   I am trying to generate a model using comparative modeling. Can
anybody suggest the quality of the model based on procheck summary.

 +--<<<  P  R  O  C  H  E  C  K S  U  M  M  A  R  Y  >>>--+
 ||
 | /var/www/PROCHECK/Jobs/7358861/7358861.pdb   1.5 1253 residues |
 ||
*| Ramachandran plot:   87.9% core   10.2% allow1.4% gener0.4% disall |
 ||
*| All Ramachandrans:   67 labelled residues (out of1235) |
+| Chi1-chi2 plots:  3 labelled residues (out of 771) |
 | Side-chain params:5 better 0 inside  0 worse   |
 ||
*| Residue properties: Max.deviation: 4.9  Bad contacts:0 |
*| Bond len/angle:9.9Morris et al class:  1  1  2 |
 ||
 | G-factors   Dihedrals:  -0.13  Covalent:  -0.07Overall:  -0.10 |
 ||
*| Planar groups:90.0% within limits  10.0% highlighted  13 off graph |
 ||
 ++
   + May be worth investigating further.  * Worth investigating further.



Thanks,



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[ccp4bb] post-doctoral position in New York

2020-08-14 Thread Goran Bajic 
Hi all,

We are looking for an enthusiastic post-doctoral fellow with experience in
cryo-EM to join our group at the Department of Microbiology at Mount Sinai
in New York City.

We use structural biology, virology and immunology approaches to answer
fundamental, mechanistic questions in immune responses to viral pathogens.
The position is for a post-doctoral fellow interested in biophysical
studies of B-cell receptor complexes and antibody responses to influenza,
SARS-CoV-2 and other viruses.

We have ample access to state-of-the-art electron microscopes through the
New York Structural Biology Center, of which Mount Sinai is a member
institution, as well as access to synchrotron radiation for X-ray
crystallographic studies at several national light sources.

Please reach out to Goran Bajic to apply or to learn more about the
opportunity.

https://www.bajiclab.org/
email: ba...@crystal.harvard.edu
Twitter: @gogo_science

===
Goran Bajic, Ph.D.
Department of Microbiology
Icahn School of Medicine at Mount Sinai
One Gustave L Levy Place, Box 1124
New York, New York 10029
https://www.bajiclab.org/
===



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[ccp4bb] Post-doctoral position in structural biology of host-pathogen interactions

2020-08-14 Thread Sebastian Zoll 
Post-doctoral position in structural biology of host-pathogen interactions at 
IOCB Prague
Job description
An attractive, fellowship-funded post-doctoral position is open in Dr Sebastian 
Zoll’s group at the Institute of Organic Chemistry and Biochemsitry (IOCB) in 
Prague. Dr Zoll’s group is using a combination of biochemical, biophysical, 
immunological and structural biology techniques to understand the mechanisms of 
viral entry into mammalian cells. The successful candidate will be using 
cryo-EM to determine the structure of a viral capsid protein in complex with 
its cellular receptor and characterise the interaction using biophysical 
techniques. As part of this process the applicant will also generate monoclonal 
antibody and nanobody libraries as tools as well as for therapeutic 
applications.



Requirements

-A recent PhD in structural biology or protein biochemistry/biophysics 
using at least one of the following techniques as the main method – cryo-EM, 
X-ray crystallography, small-angle X-ray scattering or NMR.

-Strong computational skills. Experience with linux operating systems 
and command line interface is required. 

-Experience in expression construct design, protein purification and 
biophysical techniques to analyse protein-protein interactions (ITC, SPR etc.).

-At least one first author publication in a high-quality, 
international, peer-reviewed journal

 
The project is supported by a multidisciplinary network of international 
collaborators and provides excellent opportunities to receive additional 
training in foreign host institutions.

The fellowship is granted for one year with possible extension by one more 
year. The earliest starting date is November 2020. The internal deadline for 
applications is 1 September 2020. For further information please see:

https://www.uochb.cz/en/iocb-fellowships 

 
The institute and the city

IOCB Prague is the leading scientific research institution in the Czech 
Republic providing a dynamic, international environment that brings together 
researchers from various fields such as structural biology, molecular biology, 
medicinal and computational chemistry.

Due to its long-standing history in applied science and strong ties with the 
pharmaceutical industry, IOCB enjoys an excellent funding situation and offers 
access to facilities for all modern structural and biophysical methods.

The IOCB cryo-EM facility housing a 300 keV high-resolution and 200 keV 
screening cryo-electron microscope will become operational next year. In the 
meanwhile IOCB researchers enjoy privileged access to the EM facilities 
(screening microscopes and Titan Krios G3) at CEITEC.

IOCB is situated near the city centre in a vibrating, historical quarter of 
Prague boasting beautiful architecture and a rich array of public amenities 
such as cafés, pubs, parks and grocery stores. Transport links by metro and 
tram are excellent with short distances to both airport as well as old town and 
Letna park with its stunning views over the Vltava river.

 
How to apply?

Please send a short motivation statement (max. 500 words), a full publication 
list and a copy of your CV to sebastian.z...@uochb.cas.cz 

2 letters of recommendation will be requested from short-listed candidates 
after the first round of application.

 
Feel free to contact Sebastian for informal enquiries.

Dr Sebastian Zoll

Junior Group Leader

Institute of Organic Chemistry and Biochemistry

Czech Academy of Sciences

Flemingovo namesti 542/2, 166 10 Prague 6

Czech Republic

Phone: +420 220 183 591

Email: sebastian.z...@uochb.cas.cz

Facebook: https://www.facebook.com/IOCBPrague













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[ccp4bb] Launching the Instruct-ERIC webinar series – 18 Aug: ‘Crowdsourcing for SARS-CoV-2 Mpro inhibitor’ and ‘Line-FRAP’

2020-08-14 Thread Claudia Alén Amaro 


Join us for the launch of the Instruct-ERIC webinar series: from structure to 
function.

[Instruct-ERIC logo]

[Instruct-ERIC]   [LinkedIn] 
 [Twitter] 


Dear Claudia

Join us for the launch of the Instruct-ERIC webinar series: from structure to 
function.



[https://instruct-eric.eu/upload/AteDC0R5yn5H4FQEQziILZtUzog9Ytua.png]



Registration is open for the first webinar in the series, which will be hosted 
by Instruct Centre Israel at the 
Weizmann Institute of Science, on 18 
August 2020 from 11:00 – 12:30 CEST.

Questions can be submitted in advance of the webinar by sending them to 
co...@instruct-eric.eu.



Register now



Talk 1: Crowdsourcing for SARS-CoV-2 Mpro inhibitor - a global effort driven by 
structural biology

Speaker: Dr Nir London



Talk 2: Line-FRAP, a method to measure diffusion rates of a large range of 
molecules in vitro and in vivo

Speaker: Prof Gideon Schreiber



Moderator: Prof Joel L Sussman

View full abstracts



We hope that you can join us on 18 August 2020 - please feel free to share this 
message with anyone who might be interested in attending the webinar.



Best wishes,

Instruct-ERIC Hub Team

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Dr Claudia Alén Amaro
Senior Project Manager

[instructlogo]

Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, OX4 2JY, 
UK.
Telephone: +44 (0) 1865 987629 +44 (0) 7494060412
Website: instruct-eric.eu
Twitter: @instructhub



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