[ccp4bb] Lecturer/Assistant Professor in Protein Structural Biology, UCD School of Biomolecular and Biomedical Science, Permanent

[Jana Haase]

Dear all, 

Applications are invited for a permanent post of a Lecturer/Assistant Professor 
in Protein Structural Biology within UCD School of Biomolecular and Biomedical 
Science. Further detail can be found at 
https://my.corehr.com/pls/coreportal_ucdp/apply?id=017183. Alternatively, go to 
https://www.ucd.ie/workatucd/jobs/ (search jobs for EXTERNAL applicants, Ref 
number: 017183).

Closing date: 12:00 noon (local Irish time) on the 3rd of June 2024



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[ccp4bb] 2024 Applied Crystallization Workshop

[Sarah Bowman]

Hi CCP4,

Announcing the Applied Crystallization Workshop at the National Crystallization 
Center at HWI in Buffalo, NY, USA.  Does your macromolecular crystallization 
project feel like the Wild West? Join our two-part Crystallization Workshop to 
learn to wrangle your crystals!

What is it? A macromolecular crystallization workshop

  *   One day virtual component on May 23 2024 (register here: 
https://us06web.zoom.us/meeting/register/tZclfuGpqDgvHNZNhBxWgGA2wT4zdd5AuDsW)

  *   Two separate 1.5 day on-site components in June OR August 2024 (apply 
here: https://forms.gle/y1BYJazpY5gsMoj9A)
Who is it for? Open to researchers at all levels: students, postdocs, PIs

Favored applicants for on-site workshop will have submitted samples for 
high-throughput screening prior to the virtual workshop and have a sample to 
bring to set up.

Deadlines:
Applications for the June 20-21 workshop must be submitted by May 6th, 2024
Applications for the August 20-21 workshop must be submitted by July 8th, 2024

For the on-site portion of the workshop, applicants must be available to travel 
on-site to Buffalo, New York during the dates of June 20-21, 2024 OR August 
20-21, 2024. On-site workshop spaces are limited and applicants will be 
selected based on suitability of project and application. Note some travel 
support is available for researchers at US-based universities.

Workshop supported by NIH R24GM141256. We gratefully acknowledge the workshop 
sponsors MiTeGen, Formulatrix, and Hampton Research.

Questions?  Reach out to us at 
hts...@hwi.buffalo.edu or check our website 
www.getacrystal.org

The National Crystallization Center Team
Sarah EJ Bowman PhD
Associate Investigator | Hauptman-Woodward Medical Research Institute
Director | National Crystallization Center | Hauptman-Woodward Medical Research 
Institute
Research Associate Professor | Department of Biochemistry and Department of 
Structural Biology |
University at Buffalo | Jacobs School of Medicine and Biomedical Sciences

Member | US National Committee for Crystallography

p: +1 716 898 8623
e: sbowman at hwi.buffalo.edu

Research Webpage
Crystallization Center Webpage

Hauptman-Woodward Medical Research Institute
700 Ellicott Street | Buffalo, NY 14203



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[ccp4bb] CCPBioSim Industry Talk - D E Shaw 29 May

[Sarah Fegan - STFC UKRI]

Dear all,



This online talk is by Brannon Batson who is a hardware design engineer at D. 
E. Shaw Research. The talk takes place on Wednesday 29 May 2024 at 15:00 UK 
time. To register visit https://www.ccpbiosim.ac.uk/deshaw2024.



Title: Using specialized hardware pipelines to massively accelerate molecular 
dynamics simulations in Anton 3



Abstract: At D. E. Shaw Research, we have designed and built multiple 
generations of highly successful special-purpose supercomputers for molecular 
dynamics simulations.  The newest generation, Anton 3, achieves simulation 
speeds at least 100-fold faster than any other currently available 
supercomputer on a wide range of biomolecular systems.  Anton machines are an 
essential foundational technology for our scientific and drug discovery 
efforts.  This talk will describe how we co-design hardware, software, and 
algorithms to accelerate both research and drug discovery, focusing on how 
specialized hardware pipelines contribute to the enormous speedups that Anton 
machines achieve.



Best wishes,

Sarah



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[ccp4bb] Coming soon: Annotation of Protein Modifications in the PDB

[Deborah Harrus]

Dear all,

The standardization of protein modification handling ensures that there 
is a single correct approach to handling each protein modification that 
occurs within the PDB archive. However, there are many existing PDB 
entries that contain protein modifications which do not follow these 
handling conventions.


As part of the protein modifications remediation project, all model 
coordinates files containing protein modifications are being re-released 
to add a new protein modification data category. This new category will 
list all observed PCMs/PTMs within the entry, as well as their type and 
category, allowing better findability.


A new category will also be added to the Chemical Component Definition 
(CCD) files. It will state whether the CCD is a known PCM, its type and 
category, as well as on which positions in the amino acid and in the 
polypeptide it is expected to be observed. If this PCM is also a known 
PTM, it will have the Uniprot generic PTM accession ID.


Finally, any protein modifications that are inconsistently handled 
within a PDB entry will be amended, to ensure that a given modification 
is consistently handled in the PDB archive.


Detailed information about this work is available from GitHub, including 
PDBx/mmCIF dictionary extension and a set of example files, and complete 
documentation of the additional annotation: 
https://github.com/wwPDB/protein-modification-extension


Questions or feedback? Contact deposit-h...@mail.wwpdb.org.

The protein chemical modifications (PCMs) and post translational 
modifications (PTMs) remediation project is a wwPDB collaborative 
project carried out principally by PDBe at EMBL-EBI, and is funded by 
BBSRC grant number BB/V018779/1.


Read this news online 



Kind regards,

Deborah Harrus, on behalf of the wwPDB

--
---
Deborah Harrus, Ph.D.
PDBe Archive Project Leader, Biocuration Lead
PDBe - Protein Data Bank in Europe

European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD UK

http://www.PDBe.org
---



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[ccp4bb] Researcher position (Structural biology of proteolipid membranes) in Bergen (Norway)

[Petri Kursula]

Dear all,

we have an opening for a researcher position at the University of Bergen. 
Funding currently exists for 1.5 years, with a starting date as soon as 
possible.

The project deals with the assembly of proteolipid multilayers, involving 
studies of integral and peripheral membrane proteins and lipid membranes using 
methods of structural biology and biophysical assays. The work will be carried 
out as a part of a larger team funded by the Research Council of Norway and the 
Faculty of Medicine, and fine details of the project depend also on the 
background of the candidate. 

For more information, see the advert: 
https://www.jobbnorge.no/en/available-jobs/job/262539/researcher-in-structural-biology-of-proteolipid-membranes
   

Applications will only be accepted via the online portal, with all mandatory 
attachments in place. Application deadline: May 14. 

With kind regards,
Petri

Petri Kursula
--
Professor 
--
Department of Biomedicine
University of Bergen, Norway
https://www.uib.no/en/persons/Petri.Kursula
petri.kurs...@uib.no 
--
Faculty of Biochemistry and Molecular Medicine
Biocenter Oulu
University of Oulu, Finland
--




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