Re: [ccp4bb] searching for ligands with double conformation

[Deborah Harrus]

Dear Anat,

Replying on behalf of Chris Thorpe:

The only reliable way I've found is to compare the conformations in each 
of the biological units and also to look for ALTLOCs. Obviously you can 
automate all of this, using BioPandas to compare peptide conformations 
(looking at position level RMSDs) and having some BioPython/Pymol code 
to deal with ALTLOCs and split them into different files.


Hope that helps!

Kind regards,

Deborah

On 24/06/2024 10:31, Anat Bashan wrote:


Dear CCP4 community,

I am interested in searching in the PDB for ligands that are in 
complex with proteins in the PDB that were deposited with a double 
conformation.


Does anyone know how to run such a search? How to define it?

Thanks a lot for your help,

Anat.

=
Anat Bashan , Ph.D Tel:972-8-9344289 
Senior staff scientist @The Ribosome Group

The Weizmann Institute of Science
The Department of Chemical and Structural Biology Mobile:972-52-3347229
Rehovot 7610001   e-mail: 
anat.bas...@weizmann.ac.il 


Israel

=




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--
---
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] searching for ligands with double conformation

[Anat Bashan]

Dear CCP4 community,

I am interested in searching in the PDB for ligands that are in complex with 
proteins in the PDB that were deposited with a double conformation.
Does anyone know how to run such a search? How to define it?

Thanks a lot for your help,
Anat.

=
Anat Bashan , Ph.D  
Tel:972-8-9344289
Senior staff scientist @The Ribosome Group
The Weizmann Institute of Science
The Department of Chemical and Structural BiologyMobile:972-52-3347229
Rehovot7610001  
 e-mail: anat.bas...@weizmann.ac.il
Israel
=








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https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1

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