[ccp4bb] Multiple Structural & biophysical roles at GSK R, Stevenage, UK

2021-08-06 Thread Chun-wa Chung 
Title : Multiple Structural and Biophysical Scientists Roles at GSK R, 
Stevenage,UK.

We have multiple openings for talented structural & biophysical scientists to 
join GSK's UK Structural & Biophysical Sciences group at Stevenage.
So if the opportunity to join a multi-disciplinary department to provide 
molecular insights into both small molecule and biopharmaceutical drug 
discovery excites you please do take a look.
286898  Post-Doctoral Research Associate - Cryo-EM Data Analysis, closes 10th 
August:
Post-Doctoral Research Associate - Cryo-EM Data Analysis in Stevenage, United 
Kingdom | GSK 
Careers

300069 Cryo-EM Scientist - processing expert, closes 27th August :
Cryo-EM Scientist in Stevenage, United Kingdom | GSK 
Careers

300367 Biophysicist with SPR experience, closes 
27th August :
Crystallisation and Biophysicist in Stevenage, 
United Kingdom | GSK 
Careers
(Please note we have two roles, this links to 
the biophysics focused role, a separate role with a crystallisation focus will 
be coming out shortly)


Thanks for reading this.
Best wishes,
Chun-wa


Chun-wa Chung
UK Head Structural & Biophysics  Sciences
GlaxoSmithKline R
Stevenage
SG1 2NY
 email : chun-wa.h.ch...@gsk.com



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Re: [ccp4bb] off-topic: structural motif / domain comparison

2021-08-06 Thread Bernhard Rupp 
A lesser known service with very powerful search across domains and chains is 

TopSearch by Manfred Sippl & Cie.:

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

 

Its training set includes PDB entries up to 2018.

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of Sam Tang
Sent: Thursday, August 5, 2021 23:43
To: CCP4BB@JISCMAIL.AC.UK
Subject: [ccp4bb] off-topic: structural motif / domain comparison

 

Dear all

 

Sorry for an off-topic question here. I wonder if anyone may be aware of any 
search program which allows one to 'blast' a protein domain just like we 
'blast' a protein sequence? For example I have an epitope in hand and would 
like to find out whether this also exists in other proteins. Most programs I 
accessed are based on sequence similarity but is there any program which 
searches a structure against a database of structures?

 

BRs

 

Sam

 

  _  

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Re: [ccp4bb] off-topic: structural motif / domain comparison

2021-08-06 Thread orly avraham 
You might also find use in databases such as pfam, ecod, cath, scop.

Orly

On Fri, Aug 6, 2021, 09:43 Sam Tang  wrote:

> Dear all
>
> Sorry for an off-topic question here. I wonder if anyone may be aware of
> any search program which allows one to 'blast' a protein domain just like
> we 'blast' a protein sequence? For example I have an epitope in hand and
> would like to find out whether this also exists in other proteins. Most
> programs I accessed are based on sequence similarity but is there any
> program which searches a structure against a database of structures?
>
> BRs
>
> Sam
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] refmac - use weighting term - pdb to mmcif

2021-08-06 Thread Marina Gárdonyi 

I deleted a line in the keyword file which was "pdbout format mmcif".

It was my first try to convert the pdb file to an mmcif file, but it  
did not work!


Best
Marina


Zitat von "Krieger, James M" :


It could be good to say how you solved it for future users.

Best wishes
James

On Aug 6, 2021, at 09:27, Marina Gárdonyi  
<652c4b26eb10-dmarc-requ...@jiscmail.ac.uk> wrote:


Hi,

as it is often the case, the mail is out and you are able to solve  
the problem on your own. Thanks anyway!


Best
Marina

Zitat von Marina Gárdonyi <652c4b26eb10-dmarc-requ...@jiscmail.ac.uk>:


Hi,

before I will soon finish my PhD, I have to solve one more problem.

I managed to refine occupancies and tls in Refmac. I also found  
out that you can use pdb-extract to convert the pdb file to an  
mmcif file so that you can validate the structure using the  
validation server.
However, during validation, it came out that the bond lengths and  
angles are hugely different from the expected values. I had used  
the automatic weighting until then. If I do the weighting by hand  
(I tried different weighting terms), I cannot convert the pdb file  
into an mmcif file anymore, because the pdb file has a different  
structure and pdb-extract does not recognize the pdb file as such.


Does anyone know the problem and can help me?

Best
Marina

--
Marina Gárdonyi

PhD Student, Research Group Professor Dr. Klebe

Department of Pharmaceutical Chemistry

Philipps-University Marburg

Marbacher Weg 6, 35032 Marburg, Germany

Phone: +49 6421 28 21392

E-Mail: marina@pharmazie.uni-marburg.de

https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.agklebe.de%2Fdata=04%7C01%7Ckriegerj%40PITT.EDU%7C56a251f8bbd547f3837b08d958b40aee%7C9ef9f489e0a04eeb87cc3a526112fd0d%7C1%7C1%7C637638352575981454%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000sdata=oLpz7kaDDGV4UF6wD%2B7mpvkZEmzuA4Bg0aoR0JtLkxk%3Dreserved=0



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--
Marina Gárdonyi

PhD Student, Research Group Professor Dr. Klebe

Department of Pharmaceutical Chemistry

Philipps-University Marburg

Marbacher Weg 6, 35032 Marburg, Germany

Phone: +49 6421 28 21392

E-Mail: marina@pharmazie.uni-marburg.de

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Re: [ccp4bb] off-topic: structural motif / domain comparison

2021-08-06 Thread Dalibor Košek 
Perhaps DALI can be of use
http://ekhidna2.biocenter.helsinki.fi/dali/

Dal.

pá 6. 8. 2021 v 8:42 odesílatel Sam Tang  napsal:

> Dear all
>
> Sorry for an off-topic question here. I wonder if anyone may be aware of
> any search program which allows one to 'blast' a protein domain just like
> we 'blast' a protein sequence? For example I have an epitope in hand and
> would like to find out whether this also exists in other proteins. Most
> programs I accessed are based on sequence similarity but is there any
> program which searches a structure against a database of structures?
>
> BRs
>
> Sam
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] off-topic: structural motif / domain comparison

2021-08-06 Thread Chris Fage 
Hi Sam,

Perhaps the Modeller service is what you’re looking for?

https://salilab.org/modeller/

Best wishes,
Chris


On Fri, 6 Aug 2021 at 07:42 Sam Tang  wrote:

> Dear all
>
> Sorry for an off-topic question here. I wonder if anyone may be aware of
> any search program which allows one to 'blast' a protein domain just like
> we 'blast' a protein sequence? For example I have an epitope in hand and
> would like to find out whether this also exists in other proteins. Most
> programs I accessed are based on sequence similarity but is there any
> program which searches a structure against a database of structures?
>
> BRs
>
> Sam
>
> --
>
> To unsubscribe from the CCP4BB list, click the following link:
> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1
>



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Re: [ccp4bb] AI papers in experimental macromolecular structure determination

2021-08-06 Thread Rangana Warshamanage 
Not sure someone already mentioned these (highly likely)

https://www.nature.com/articles/s41586-019-1923-7
https://www.nature.com/articles/s41586-021-03819-2
https://science.sciencemag.org/content/early/2021/07/19/science.abj8754


On Tue, Aug 3, 2021 at 12:53 PM Thorn, Dr. Andrea <
andrea.th...@uni-hamburg.de> wrote:

> Dear colleagues,
>
> I have compiled a list of papers that cover the application of AI/machine
> learning methods in single-crystal structure determination (mostly
> macromolecular crystallography) and single-particle Cryo-EM. The draft list
> is attached below.
>
>
>
> If I missed any papers, please let me know. I will send the final list
> back here, for the benefit of all who are interested in the topic.
>
>
>
> Best wishes,
>
>
>
>
>
> Andrea.
>
>
>
>
>
> __
>
> General:
>
> - Gopalakrishnan, V., Livingston, G., Hennessy, D., Buchanan, B. &
> Rosenberg, J. M. (2004). Acta Cryst D. 60, 1705–1716.
>
> - Morris, R. J. (2004). Acta Cryst D. 60, 2133–2143.
>
>
>
> Micrograph preparation:
>
> - (2020). Journal of Structural Biology. 210, 107498.
>
>
>
> Particle Picking:
>
> - Sanchez-Garcia, R., Segura, J., Maluenda, D., Carazo, J. M. & Sorzano,
> C. O. S. (2018). IUCrJ. 5, 854–865.
>
> - Al-Azzawi, A., Ouadou, A., Tanner, J. J. & Cheng, J. (2019). BMC
> Bioinformatics. 20, 1–26.
>
> - George, B., Assaiya, A., Roy, R. J., Kembhavi, A., Chauhan, R., Paul,
> G., Kumar, J. & Philip, N. S. (2021). Commun Biol. 4, 1–12.
>
> - Lata, K. R., Penczek, P. & Frank, J. (1995). Ultramicroscopy. 58,
> 381–391.
>
> - Nguyen, N. P., Ersoy, I., Gotberg, J., Bunyak, F. & White, T. A. (2021).
> BMC Bioinformatics. 22, 1–28.
>
> - Wang, F., Gong, H., Liu, G., Li, M., Yan, C., Xia, T., Li, X. & Zeng, J.
> (2016). Journal of Structural Biology. 195, 325–336.
>
> - Wong, H. C., Chen, J., Mouche, F., Rouiller, I. & Bern, M. (2004).
> Journal of Structural Biology. 145, 157–167.
>
>
>
> Motion description in Cryo-EM:
>
> - Matsumoto, S., Ishida, S., Araki, M., Kato, T., Terayama, K. & Okuno, Y.
> (2021). Nat Mach Intell. 3, 153–160.
>
> - Zhong, E. D., Bepler, T., Berger, B. & Davis, J. H. (2021). Nat Methods.
> 18, 176–185.
>
>
>
> Local resolution:
>
> - Avramov, T. K., Vyenielo, D., Gomez-Blanco, J., Adinarayanan, S.,
> Vargas, J. & Si, D. (2019). Molecules. 24, 1181.
>
> - Ramírez-Aportela, E., Mota, J., Conesa, P., Carazo, J. M. & Sorzano, C.
> O. S. (2019). IUCrJ. 6, 1054–1063.
>
> - (2021). QAEmap: A Novel Local Quality Assessment Method for Protein
> Crystal Structures Using Machine Learning.
>
>
>
> Map post-processing:
>
> - Sanchez-Garcia, R., Gomez-Blanco, J., Cuervo, A., Carazo, J. M.,
> Sorzano, C. O. S. & Vargas, J. (2020). BioRxiv. 2020.06.12.148296.
>
>
>
> Secondary structure assignment in map:
>
> - Subramaniya, S. R. M. V., Terashi, G. & Kihara, D. (2019). Nat Methods.
> 16, 911–917.
>
> - Li, R., Si, D., Zeng, T., Ji, S. & He, J. (2016). 2016 IEEE
> International Conference on Bioinformatics and Biomedicine (BIBM), Vol. pp.
> 41–46.
>
> - Si, D., Ji, S., Nasr, K. A. & He, J. (2012). Biopolymers. 97, 698–708.
>
> - He, J. & Huang, S.-Y. Brief Bioinform.
>
> - Lyu, Z., Wang, Z., Luo, F., Shuai, J. & Huang, Y. (2021). Frontiers in
> Bioengineering and Biotechnology. 9,.
>
> - Mostosi, P., Schindelin, H., Kollmannsberger, P. & Thorn, A. (2020).
> Angewandte Chemie International Edition.
>
>
>
> Automatic structure building:
>
> - Alnabati, E. & Kihara, D. (2020). Molecules. 25, 82.
>
> - Si, D., Moritz, S. A., Pfab, J., Hou, J., Cao, R., Wang, L., Wu, T. &
> Cheng, J. (2020). Sci Rep. 10, 1–22.
>
> - Moritz, S. A., Pfab, J., Wu, T., Hou, J., Cheng, J., Cao, R., Wang, L. &
> Si, D. (2019).
>
> - Chojnowski, G., Pereira, J. & Lamzin, V. S. (2019). Acta Cryst D. 75,
> 753–763.
>
>
>
> Crystallization:
>
> - Liu, R., Freund, Y. & Spraggon, G. (2008). Acta Cryst D. 64, 1187–1195.
>
> - (2004). Methods. 34, 390–407.
>
> - Bruno, A. E., Charbonneau, P., Newman, J., Snell, E. H., So, D. R.,
> Vanhoucke, V., Watkins, C. J., Williams, S. & Wilson, J. (2018). PLOS ONE.
> 13, e0198883.
>
>
>
> Crystal centering:
>
> - Ito, S., Ueno, G. & Yamamoto, M. (2019). J Synchrotron Rad. 26,
> 1361–1366.
>
> - Crystal centering using deep learning in X-ray crystallography.
>
> - Elbasir, A., Moovarkumudalvan, B., Kunji, K., Kolatkar, P. R., Mall, R.
> & Bensmail, H. (2019). Bioinformatics. 35, 2216–2225.
>
>
>
> Diffraction image analysis:
>
> - Czyzewski, A., Krawiec, F., Brzezinski, D., Porebski, P. J. & Minor, W.
> (2021). Expert Systems with Applications. 174, 114740.
>
>
>
> Peak search in serial crystallography:
>
> Ke, T.-W., Brewster, A. S., Yu, S. X., Ushizima, D., Yang, C. & Sauter, N.
> K. (2018). J Synchrotron Rad. 25, 655–670.
>
>
>
> Space group assignment from diffraction image (small molecules):
>
> Aguiar, J. A., Gong, M. L., Unocic, R. R., Tasdizen, T. & Miller, B. D.
> (2019). Science Advances. 5, eaaw1949.
>
>
>
> Data quality assessment in MX:
>
> - Vollmar, M., Parkhurst, J. M., Jaques, D., Baslé,

Re: [ccp4bb] refmac - use weighting term - pdb to mmcif

2021-08-06 Thread Marina Gárdonyi 

Hi,

as it is often the case, the mail is out and you are able to solve the  
problem on your own. Thanks anyway!


Best
Marina

Zitat von Marina Gárdonyi <652c4b26eb10-dmarc-requ...@jiscmail.ac.uk>:


Hi,

before I will soon finish my PhD, I have to solve one more problem.

I managed to refine occupancies and tls in Refmac. I also found out  
that you can use pdb-extract to convert the pdb file to an mmcif  
file so that you can validate the structure using the validation  
server.
However, during validation, it came out that the bond lengths and  
angles are hugely different from the expected values. I had used the  
automatic weighting until then. If I do the weighting by hand (I  
tried different weighting terms), I cannot convert the pdb file into  
an mmcif file anymore, because the pdb file has a different  
structure and pdb-extract does not recognize the pdb file as such.


Does anyone know the problem and can help me?

Best
Marina

--
Marina Gárdonyi

PhD Student, Research Group Professor Dr. Klebe

Department of Pharmaceutical Chemistry

Philipps-University Marburg

Marbacher Weg 6, 35032 Marburg, Germany

Phone: +49 6421 28 21392

E-Mail: marina@pharmazie.uni-marburg.de

http://www.agklebe.de/



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--
Marina Gárdonyi

PhD Student, Research Group Professor Dr. Klebe

Department of Pharmaceutical Chemistry

Philipps-University Marburg

Marbacher Weg 6, 35032 Marburg, Germany

Phone: +49 6421 28 21392

E-Mail: marina@pharmazie.uni-marburg.de

http://www.agklebe.de/



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[ccp4bb] refmac - use weighting term - pdb to mmcif

2021-08-06 Thread Marina Gárdonyi 

Hi,

before I will soon finish my PhD, I have to solve one more problem.

I managed to refine occupancies and tls in Refmac. I also found out  
that you can use pdb-extract to convert the pdb file to an mmcif file  
so that you can validate the structure using the validation server.
However, during validation, it came out that the bond lengths and  
angles are hugely different from the expected values. I had used the  
automatic weighting until then. If I do the weighting by hand (I tried  
different weighting terms), I cannot convert the pdb file into an  
mmcif file anymore, because the pdb file has a different structure and  
pdb-extract does not recognize the pdb file as such.


Does anyone know the problem and can help me?

Best
Marina

--
Marina Gárdonyi

PhD Student, Research Group Professor Dr. Klebe

Department of Pharmaceutical Chemistry

Philipps-University Marburg

Marbacher Weg 6, 35032 Marburg, Germany

Phone: +49 6421 28 21392

E-Mail: marina@pharmazie.uni-marburg.de

http://www.agklebe.de/



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Re: [ccp4bb] off-topic: structural motif / domain comparison

2021-08-06 Thread Jan Dohnalek 
Like PDBeFOLD search?
https://www.ebi.ac.uk/msd-srv/ssm/

Jan


On Fri, Aug 6, 2021 at 8:43 AM Sam Tang  wrote:

> Dear all
>
> Sorry for an off-topic question here. I wonder if anyone may be aware of
> any search program which allows one to 'blast' a protein domain just like
> we 'blast' a protein sequence? For example I have an epitope in hand and
> would like to find out whether this also exists in other proteins. Most
> programs I accessed are based on sequence similarity but is there any
> program which searches a structure against a database of structures?
>
> BRs
>
> Sam
>
> --
>
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-- 
Jan Dohnalek, Ph.D
Institute of Biotechnology
Academy of Sciences of the Czech Republic
Biocev
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252 50 Vestec near Prague
Czech Republic

Tel. +420 325 873 758



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[ccp4bb] off-topic: structural motif / domain comparison

2021-08-06 Thread Sam Tang 
Dear all

Sorry for an off-topic question here. I wonder if anyone may be aware of
any search program which allows one to 'blast' a protein domain just like
we 'blast' a protein sequence? For example I have an epitope in hand and
would like to find out whether this also exists in other proteins. Most
programs I accessed are based on sequence similarity but is there any
program which searches a structure against a database of structures?

BRs

Sam



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