[ccp4bb] Post-doctoral vacancy in cryoEM of viruses

[Hasan, Syed Saif]

Dear Colleagues,

A vacancy for a post-doctoral researcher is available immediately in my lab in 
the University of Maryland Center for Biomolecular Therapeutics located on the 
campus of Institute for Bioscience and Biotechnology Research (IBBR; 
https://www.ibbr.umd.edu/profiles/s-saif-hasan) in Rockville MD. We use 
high-resolution single particle cryoEM and X-ray crystallography to investigate 
how viruses utilize structural similarities with host proteins to hijack 
inter-organelle communication.

Prior experience in insect cell culture for recombinant protein production is 
desirable. Expertise in cryoEM or X-ray crystallography will be advantageous. 
Candidates who have recently completed their PhD are encouraged to apply.

IBBR is located 20 miles north-west of Washington DC. In IBBR, you will have 
in-house access to a 200 kV Talos Arctica with a Falcon 3EC DED and a 200 kV 
Glacios with a K3 DED and a Volta Phase Plate (VPP). We have a Vitrobot Mark IV 
and a Cp3 cryo-plunger for sample preparation. We have off-site access to a 
Titan Krios microscope equipped with DED and VPP. For X-ray crystallography, we 
have access to a Mosquito crystallization robot. Data collection is usually 
performed at synchrotrons. Our research is highly collaborative and is 
supported by wonderful colleagues who help us out with their expertise in NMR 
spectroscopy, lipidomics, HDX-MS, MD simulations, computer assisted drug 
design, and cellular imaging.

Interested candidates should send their CV and a cover letter to me at 
ssha...@som.umaryland.edu


The University of Maryland, Baltimore is an Equal Opportunity, Affirmative 
Action employer. Minorities, women, individuals with disabilities and protected 
veterans are encouraged to apply.


Saif

S. Saif Hasan, PhD
Assistant Professor
Department of Biochemistry and Molecular Biology, University of Maryland School 
of Medicine
108 N. Greene Street, Baltimore MD 21201
https://www.medschool.umaryland.edu/profiles/Hasan-S-Saif-Hasan-Syed-Saif/

Associate Member
Program in Oncology, University of Maryland Marlene and Stewart Greenebaum 
Comprehensive Cancer Center (UMGCCC)
22 S. Greene Street, Baltimore MD 21201

Office and Laboratory Address:
Center for Biomolecular Therapeutics, Institute for Bioscience and 
Biotechnology Research (IBBR)
9600 Gudelsky Drive, Rockville MD 20850
https://www.ibbr.umd.edu/profiles/s-saif-hasan
Phone: 240-314-6396
Fax: 240-314-6225






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[ccp4bb] Scientific Web Application Developer Opportunity at RCSB/PDB (Rutgers)

[john.westbr...@rcsb.org]

Scientific Web Application Developer (RCSB/PDB Rutgers)

Summary

We are looking for a full-stack developer with a minimum of five years experience using modern database and web technologies. The 
candidate should enjoy engaging with other developers and scientists in a collaborative team environment.


The work at the PDB focuses on data analysis and transformation, and the presentation and visualization of data using complex 
interactive graphical user interfaces. An important aspect of the work is to provide our users with the ability to search and 
explore the data in the PDB Archive. Solutions are implemented using a wide range of custom components developed and maintained at 
the RCSB PDB, in addition to third-party tools, libraries, frameworks and technologies.


The candidate should be comfortable working in a fast-changing environment, and be able to demonstrate an ability to think 
creatively, generate new ideas, and implement solutions. The candidate should also show an eagerness and willingness to learn new 
skills and master new technologies.


The team at RCSB consists of a group of highly-skilled bio-curators, scientists, software developers, designers, and educators, 
working in a lively and fast-paced environment.


The successful candidate will be able to take full advantage of the benefits of working at an academic institution. Employees are 
encouraged to engage in professional development, either by attending seminars and training workshops, or by enrolling, 
tuition-free, in courses provided by Rutgers.

Requirements

Ideally the candidate should have in-depth experience with several of the following technologies, languages, and frameworks, or have 
experience with comparable or related technologies:


Relational and document databases (MySQL, MongoDB), search tools (ElasticSearch, GraphQL), Java, Python, Javascript, JSON, 
React/Redux, Node.js, JQuery, HTML, Git, shell scripting, use of modern IDEs.


Any scientific background would be considered a plus, especially experience in any of the following areas: Molecular Biology, 
Bioinformatics, Biochemistry, Chemistry, Genomics. Experience working with large and complex scientific datasets would also be a plus.


While a scientific background is not a requirement for the position, the candidate should be able to demonstrate a willingness and 
ability to engage with scientists and scientific content, and be interested in working in an academic/research environment.

Job Description

Responsibilities for this position will include:

Design, development and deployment of modern, scalable, reusable 
web-applications.
Analysis, refactoring and adaptation of legacy code to conform to new 
architecture designs.
Development of complex interactive graphical user interfaces.
Debugging, testing, troubleshooting.
Use of and development of automated testing suites.

Qualifications:

Masters or B.Sc degree in Computer Science, Biochemistry, Bioinformatics, or a related discipline, or a comparable combination 
of education and experience developing modern Scientific Web applications.

Excellent interpersonal, verbal and written communication skills.

Apply at Rutgers:

jobs.rutgers.edu/postings/105869

--
John Westbrook
RCSB, Protein Data Bank
Rutgers, The State University of New Jersey
Institute for Quantitative Biomedicine at Rutgers
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
e-mail: john.westbr...@rcsb.org
Ph: (848) 445-4290 Fax: (732) 445-4320



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[ccp4bb] Job opportunities with Oxfords Biomedical Research Computing facility

[Robert Esnouf]

Dear All,

Please feel free to share this email with anyone who might be interested... The 
first post in particular might be of interest to structural biologists with a 
strong computing background who are interested into moving into research 
computing as a career...

I hope you have all been keeping safe in this most difficult of years. It is 
especially important this year to make the most of the season and take some 
time out for your nearest and dearest - even if you are still keeping a secret 
eye on things really.

Oxford's Biomedical Research Computing (BMRC), the compute facility of the 
Wellcome Centre for Human Genetics and the Oxford Big Data Institute, has been 
busy with the best of you, but now it is time to expand our team of five ready 
for future challenges... So, if joining a growing team at the heart of some 
truly fantastic research - including lots of world-leading Covid-19 research - 
appeals then read on...

First, we are looking for a Grade 7 Research Computing Administrator to join 
the team based in the Wellcome Centre for Human Genetics. The role will be 
mostly directly supporting users in getting their science done and will have a 
particular role supporting the electron microscopy (EM) research of the Centre. 
This role would be an ideal stepping-stone into research computing for someone 
with a strong background in scientific computing, especially in the research 
areas of BMRC, rather than requiring a high level of hardware knowledge at the 
outset - the closing date for this post is Monday 18th January

https://my.corehr.com/pls/uoxrecruit/erq_jobspec_version_4.display_form?p_company=10_internal_external=E_display_in_irish=N_process_type=_applicant_no=_form_profile_detail=_display_apply_ind=Y_refresh_search=Y_recruitment_id=148898

Second, we are advertising for a Grade 7 Information Governance Officer based 
in the Big Data Institute to help with all aspects of our compliance, but 
especially for our on-premise cloud-based services, so that we can bring new 
areas of research to our platforms. The role will be particularly supporting 
the Novartis-Oxford collaboration in data science and AI and the research of 
the National Consortium of Intelligent Medical Imaging (NCIMI) - the closing 
date for this post is Monday 11th January

https://my.corehr.com/pls/uoxrecruit/erq_jobspec_version_4.display_form?p_company=10_internal_external=E_display_in_irish=N_process_type=_applicant_no=_form_profile_detail=_display_apply_ind=Y_refresh_search=Y_recruitment_id=148790

Finally, our friends at the neighbouring the Kennedy Institute of Rheumatology 
are also looking for a Grade 8 Research Computing Administrator. From Easter 
2021, the Kennedy Institute will join with BMRC to develop further our 
coherent, centrally managed research computing capability. This role with 
jointly report to myself and to Brian Marsden (brian.mars...@kennedy.ox.ac.uk) 
and will partly be to directly supporting users in getting their science done 
on BMRC facilities and also to be responsible for the hardware that remains in 
the Kennedy Institute - the closing date for this post is Monday 11th January

https://my.corehr.com/pls/uoxrecruit/erq_jobspec_version_4.display_form?p_company=10_internal_external=E_display_in_irish=N_process_type=_applicant_no=_form_profile_detail=_display_apply_ind=Y_refresh_search=Y_recruitment_id=148730

After the turkey is finished and the presents unwrapped, why not unwrap your CV 
and send it in? Informal questions can be directed to me in the first instance 
or else see the individual job descriptions...

Season's Greetings and Best Wishes for a much better 2021!
Take care all,
Robert Esnouf

--

Dr Robert Esnouf

University Research Lecturer,
Director of Research Computing BDI,
Head of Research Computing Core WHG,
NDM Research Computing Strategy Officer

Main office:
Room 10/028, Wellcome Centre for Human Genetics,
Old Road Campus, Roosevelt Drive, Oxford OX3 7BN, UK

Emails:
rob...@strubi.ox.ac.uk / rob...@well.ox.ac.uk / robert.esn...@bdi.ox.ac.uk

Tel: (+44)-1865-287783 (WHG); (+44)-1865-743689 (BDI)




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[ccp4bb] Graduate student position in structural bioinformatics

[Marcus Fischer]

Dear all,

The Fischer lab at St. Jude is recruiting a computational graduate student
for a data-driven project that exploits protein flexibility and hydration
for ligand discovery (see attachment).

Application deadline is in January for admission to the PhD program in
August 2021.


Happy holidays,

Marcus


*Marcus Fischer, PhD*

*Assistant Member*

*Chemical Biology & Therapeutics*

*and Structural Biology *



*https://www.stjude.org/fischer *



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FischerSJ_compPhDstudent_2021.pdf
Description: Adobe PDF document

[ccp4bb] Position available: FragMAX postdoc (MAX IV)

[Tobias Krojer]

Dear all,

I would like to draw your attention to a 2-years postdoc position at the
FragMAX facility at MAX IV Laboratory (https://www.maxiv.lu.se)
:



*The FragMAX facility provides a user facility for crystallographic
fragment screening at BioMAX, the first operational beamline for
macromolecular crystallography at MAX IV. Our aim is to develop a platform
which enables users with different levels of experience to routinely
achieve actionable screening hits for their targets. *

*We are seeking to appoint a postdoctoral fellow for the FragMAX facility
to further develop its current capabilities. This is an exciting
opportunity for an aspiring post-doctoral fellow to join an international
and interdisciplinary team, which is part of BioMAX and the MX-group. You
will develop innovative screening protocols in order to facilitate and
accelerate fragment elaboration. This will involve conceptual planning of
suitable workflows, as well as testing and implementation of robust
experimental protocols. Moreover, you will help to establish best practice
data collection protocols for protein-ligand screening which make use of
the unique capabilities of BioMAX. You will support users during fragment
screening and other experiments and disseminate feedback in order to
improve the overall performance of the facility. You are expected to work
both independently and in close collaboration with the entire FragMAX and
BioMAX teams, as well as with academic and industrial collaboration
partners. A willingness to challenge existing paradigms and to explore new
avenues would be an asset. *


*Closing date for applications is Sunday January 17th.*



For more information and to apply see:

https://lu.varbi.com/en/what:job/jobID:371474



Best wishes
Tobias Krojer



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[ccp4bb] Reminder - Registration for CCP4 Virtual Study Weekend 2021 is now live

[McIntyre, Karen (STFC,RAL,SC)]

The CCP4 study weekend is going online for 2021! We would like to welcome you 
to join us for this year's meeting which will run from 5th-8th January. The 
theme this year is:

Integrating Structural Biology

We have invited a diverse group of speakers to give insights into different 
methodological approaches that can enrich structural understanding of chemistry 
and biology beyond our crystal structures. Talks include several subjects on 
structural bioinformatics, time resolved and dynamics studies, in cell 
measurements, biophysical approaches to quantify macromolecular interactions, 
and many other novel and established integrative approaches.

See details of the programme and registration here:

https://ccp4sw2021.meeting-mojo.com/

Registration is free this year.  We already have had ~1000 people registering 
for the CCP4 Virtual Study Weekend which will make it the largest Study Weekend 
in number of delegates ever but being a virtual event we still have plenty of 
room if you haven't already registered.  We have tried to time the programme to 
make it accessible to as many people around the world.

As is usual there will there will be a chance to find out "What's New in CCP4?" 
and the Lunch Time Bytes sessions will be happening before the main lectures 
start each day.

We also will be having social events in the evening including a pub quiz on 
5th, Two Truths and a Lie quiz on 6th, 2 socials on 7th (Crafty 
Crystallographers and Among Us! But with crystallographers) and a mini 
Minecraft tournament on 8th (to complement the Minecraft chatroom that will 
have been running all week).

There will be plenty of space for networking both on an individual basis (via 
text messaging through the hub and video messaging) and by going into "The Trip 
to CCP4" networking space where there are breakout rooms for people to interact.

Diamond Light Source will also be holding their MX User Meeting between 
09:00-11:00 GMT on Wednesday 6th January 2021.

Regards

Karen McIntyre
CCP4 Project Administrator
Science and Technology Facilities Council
RCaH 1.22
Rutherford Appleton Laboratory
Harwell Campus
Didcot
OX11 0FA

karen.mcint...@stfc.ac.uk
01235 44 5790


[cid:image003.png@01D6D78C.C5EC9DA0]

**Please note that I only work part-time until 1.30pm**


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[ccp4bb] MoRDa update

[Alexey Vagin]

Dear MoRDa users 

A new update to the package is released. This is currently available for 
standalone MoRDa installations.

In addition to regular extension of the database, the following new features 
are added to the structure solution pipeline.

1. Multimeric search models reduced to interacting domains.

This type of models is generated if MoRDa database contains a homologous homo- 
or hetero-oligomeric structure. The domains belonging to different subunits of 
that structure but making close contacts with each other, are assembled into a 
single search model. Based on this, an ensemble model is generated if selected 
domains have other homologues in the database. Such search models are relevant 
for e.g. solution of immunoglobulin structures. (Previous MoRDa versions were 
only generating non-ensemble multimeric search models composed of complete 
chains).

2. A command line option to use a search model missing from Morda database 
(e.g. a model that has not yet been deposited in the PDB).

morda  -f file_sf -s file_seq -p my_model.pdb

morda_prep  -f file_sf -s file_seq -p my_model.pdb

If my_model.pdb contains a single polypeptide chain, an attempt will be made to 
generate ensemble models adding structures from the database. If the model 
contains DNA or RNA or more than one polypeptide chain, or is an NMR model, it 
will be used as is in MR trials.

3. A few more command line options for tweaking MR trials with a particular 
model, generated or provided by the user.

Run morda_solve  -h for details.

Both update and installation instructions are available from MoRDa homepage 
.

MoRDa can be used online through ccp4cloud  and 
ccp4online .

Best wishes

Alexey





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[ccp4bb] CoSeC Impact Award 2021 - call now open

[Dawn Geatches]

Dear Member of the CCP4 Community, 
 
would you describe yourself as a Masters or PhD student, or an Early Career 
Researcher (i.e. with up to 5 years post doctoral experience at 28th February 
2021)? 

 If so, you could be eligible to apply for the 2021 (Computational Science 
Centre for Research Communities: https://www.scd.stfc.ac.uk/Pages/CoSeC.aspx)   
CoSeC Impact Award: 
https://web.cvent.com/event/2f0687c1-a924-4de8-8c48-0805fa35c641/summary
 
We would love to hear how being a member of the CoSeC community has benefitted 
your work, for example: 

• Have you solved a structure using CCP4 software that has a clear 
social or economic impact?
• Have you attended a CCP4 training course that helped you solve such a 
structure?
 
Receiving this award would be a boost to your cv, plus, there is a range of 
prizes on offer including working with us to write up your application into a 
case study  - see examples developed from this year's winning entries: 
https://www.scd.stfc.ac.uk/Pages/CoSeC_Impact_Award_Nov2020.aspx
 
Should you have any questions about the award and/or the application process, 
please contact:
 
dawn.geatc...@stfc.ac.uk
 
Thank you and Good Luck with your application!
 




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