Hi David, You can try the SPASM algorithm, specifically useful for finding and comparing spatial motifs: See its use in Figure 3 in our publication: https://onlinelibrary.wiley.com/doi/10.1002/pro.2493
And the SPASM paper: https://www.sciencedirect.com/science/article/abs/pii/S0022283698923932#:~:text=In%20general%2C%20there%20are%20two,of%20the%20method%20are%20discussed. Sincerely, Debanu On Wed, Sep 10, 2025 at 08:06 Sanders, David < 00012ead17872a05-dmarc-requ...@jiscmail.ac.uk> wrote: > Hi all, > > > > We have recently determined the structure of a protein ligand complex, > where there is a Arg/carboxylate salt bridge,, where the plane of the Arg > guanidino group is perpendicular to the plane of the carboxyl group. I’m > trying to find other examples of the same orientation, but have had little > luck (not even fully sure how to do that search !). Does anyone have any > examples of such an interaction ? > > > > Many thanks for your help, > > > > David > > > > ------------------------------------------------------------------------------------ > > Dr. David Sanders > > Department of Chemistry > > Professor of Structural Biology > > web page: https://research-groups.usask.ca/sanders/ > > Email: david.sand...@usask.ca Ph : (306) 966-6788 > > > > Mailing Address: Office > : Thorv. 153 > > Department of Chemistry Lab : Thorv. 139 > > University of Saskatchewan Lab Ph : (306) > 966-1936 > > 110 Science Place > <https://www.google.com/maps/search/110+Science+Place?entry=gmail&source=g> > Fax : (306) 966-4730 > > Saskatoon, SK, S7N 5C9, CANADA > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
