[ccp4bb] Glide grid box

[Thripthi Shenoy]

Greetings to all!

I am trying to generate a grid box over the co-crystallized ligand in
Maestro. However, the ligand is not being detected and the gridbox is
generated outside the protein-ligand complex. I tried all possible ways,
but in vain.
Any suggestions in this regard would be very helpful to me.

Thanking in advance,

With regards,
Thripthi S.



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[ccp4bb] Postdoctoral position in structural biology at the Institut Pasteur

[Pablo Guardado Calvo]

Dear all,

A two-year postdoctoral position is available in my group at the Institut
Pasteur (Paris, France). We investigate the molecular mechanism of viral
entry into target cells combining structural biology, biophysics,
computational and virology approaches. The goal is to use the resulting
information to develop vaccines and therapies. You can check our previous
work in: Serris et al. Cell (2020, PMIDs: 32937107), Guardado-Calvo et al.
Science (2017, 29097548) or Mitler et al. Science Translational Medicine
(2023, 37315110).

We are looking for a person with a good track record and an excellent
motivation to pursue a career in structural virology. The postdoctoral
fellow will be in charge of characterising protein complexes using
cryo-electron microscopy and of setting up functional assays to
characterise their activity in vitro. The group is hosted in friendly and
dynamic environment with extensive opportunities to learn new techniques
and establish collaborations. We have fully equipped P1 and P2 labs and the
Institut Pasteur is equipped with start-of-the-art microscopes, including
two 200 kV Glacios and a 300 kV Titan Krios equipped with a Falcon 4
detector and an energy filter. The synchrotron Soleil is less than 1 hour
from the Institut and we have fluid access to the crystallography and
biophysics platforms, which are excellently equipped.

Required qualifications
• A PhD in structural biology, biochemistry, biophysics or virology.
• Documented experience in at least one of the following techniques:
structural biology (cryo-electron microscopy or crystallography) or
virology (neutralisation or fusion assays).
• Good interpersonal skills

The application should contain
1. A letter of motivation (1 page) with a short description of your
research interests.
2. A CV, including a list of relevant skills, experiences and a full
publication list.
3. Names and e-mail addresses of 2-3 reference persons, indicating their
professional relation to you.

The starting date is negotiable. Ideally around February/March 2024. The
deadline for this application is the 20th December 2023.

Informal inquiries and application should be sent to Pablo Guardado-Calvo (
guard...@pasteur.fr)

For more information, just follow this link:

https://research.pasteur.fr/en/job/postdoctoral-position-in-structural-biology-of-poxviruses/



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[ccp4bb] Errors in atomic coordinates and B factors in MX

[John R Helliwell]

Dear Colleagues,I feel sure you will be interested in this topic which I have provided an overview of here:-Error estimates in atom coordinates and B factors in macromolecular crystallography - IUCr forumsforums.iucr.orgincluding a weblink to the article. I have placed this within the IUCr Forum for Public Input to the IUCr Committee on Data. The article itself is also open access.Best wishes,John Emeritus Professor John R Helliwell DSc

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[ccp4bb] A postdoctoral fellow position at Dana-Farber Cancer Institute and Harvard Medical School, Boston, USA

[Tan, Kemin]

Job Description
The Reinherz lab at Dana-Farber Cancer Institute and Harvard Medical School is 
recruiting a postdoctoral fellow to study structural immunology. We use 
interdisciplinary approaches at the interface of structural biology and the 
molecular analysis of cellular immunity with the aim of translating new 
insights into T cell cellular immunotherapies including T cell receptor designs 
and rational cancer vaccine developments.

Located in Boston and the surrounding communities, Dana-Farber Cancer Institute 
brings together world renowned clinicians, innovative researchers and dedicated 
professionals, allies in the common mission of conquering cancer, HIV/AIDS and 
related diseases. Combining extremely talented people with the best 
technologies in a genuinely positive environment, we provide compassionate and 
comprehensive care to patients of all ages; we conduct research that advances 
treatment; we educate tomorrow's physician/researchers; we reach out to 
underserved members of our community; and we work with amazing partners, 
including other Harvard Medical School-affiliated hospitals.


Responsibilities
Specific research directions include structural and molecular studies of T cell 
development and antigen recognition involving T cell receptors and pre-T cell 
receptors. The laboratory provides a full access to cutting-edge techniques in 
molecular biology, protein chemistry, NMR, and protein crystallography. Vital 
collaborations with scientists including at the Advanced Photon Source in 
Chicago are ongoing.


Qualifications

Highly motivated candidates with a recent PhD or MD/PhD in structural biology 
and significant experience in molecular biology, biochemistry, protein 
expression and with some background in immunology are encouraged to apply. 
Skills in molecular cloning, protein chemistry and crystallography and/or other 
structural approaches are essential. Candidates should have a publication 
record in peer-reviewed journals. We are seeking a candidate with excellent 
writing and communication skills, able to work independently but also 
effectively with other lab members. Applicants should include a short statement 
of research goals, CV and three references with their application.



Dana-Farber Cancer Institute is an equal opportunity employer and affirms the 
right of every qualified applicant to receive consideration for employment 
without regard to race, color, religion, sex, gender identity or expression, 
national origin, sexual orientation, genetic information, disability, age, 
ancestry, military service, protected veteran status, or other groups as 
protected by law.




Please contact Dr. Ellis Reinherz for more information.
Fax: 617-632-3351
E-mai:l ellis_reinh...@dfci.harvard.edu




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Re: [ccp4bb] Autodock vina docking results

[Thripthi Shenoy]

I am thankful and grateful to everyone for guiding me through.

Regards,
Thripthi S.

On Mon, Nov 20, 2023 at 1:50 PM Subhomoi Borkotoky 
wrote:

>   Hi,
>
> Probably you are not setting the grid right. Try the AMDock tool, it uses
> Autodock vina. Here you can specify your residues, and the grid will be
> prepared accordingly.
>
> https://github.com/Valdes-Tresanco-MS/AMDock-win
>
>
>
> Thanks & Regards,
> --
> *Subhomoi Borkotoky, Ph. D.*
> Assistant Professor
> Department of Biotechnology,
> Invertis University, Bareilly-243123,
> UP, India.
>
> Alternate E-mail:  subhomo...@invertisuniversity.ac.in
>
>
> https://scholar.google.co.in/citations?hl=en&pli=1&user=bJz7GokJ
> Web of Science Researcher ID: AAC-9193-2021
> 
>
>
> On Sun, Nov 19, 2023 at 6:05 PM Thripthi Shenoy 
> wrote:
>
>> Greetings to all,
>>
>> I have performed docking through Glide and Autodock vina for a protein
>> for which the active site has been taken from the literature. Glide is able
>> to dock the compounds correctly in the active site whereas autodock vina
>> does not dock the compounds within the specified site. I have tried docking
>> several times in Autodock vina, but not able to obtain proper results.
>> I would be grateful to receive any suggestions regarding the same.
>>
>> Thanking you in advance,
>> Thripthi S.
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>>
>



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Re: [ccp4bb] Autodock vina docking results

[Subhomoi Borkotoky]

  Hi,

Probably you are not setting the grid right. Try the AMDock tool, it uses
Autodock vina. Here you can specify your residues, and the grid will be
prepared accordingly.

https://github.com/Valdes-Tresanco-MS/AMDock-win



Thanks & Regards,
--
*Subhomoi Borkotoky, Ph. D.*
Assistant Professor
Department of Biotechnology,
Invertis University, Bareilly-243123,
UP, India.

Alternate E-mail:  subhomo...@invertisuniversity.ac.in


https://scholar.google.co.in/citations?hl=en&pli=1&user=bJz7GokJ
Web of Science Researcher ID: AAC-9193-2021



On Sun, Nov 19, 2023 at 6:05 PM Thripthi Shenoy 
wrote:

> Greetings to all,
>
> I have performed docking through Glide and Autodock vina for a protein
> for which the active site has been taken from the literature. Glide is able
> to dock the compounds correctly in the active site whereas autodock vina
> does not dock the compounds within the specified site. I have tried docking
> several times in Autodock vina, but not able to obtain proper results.
> I would be grateful to receive any suggestions regarding the same.
>
> Thanking you in advance,
> Thripthi S.
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1
>



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