Re: [ccp4bb] Looking for method to find similar oligomeric arrangement

[Boaz Shaanan]

Hi, You can try the SSM from the pdbe tools, also described in Krissinel and Henrick (2004), Acta D63, 366-380. It worked for us nicely on a similar problem of a dimeric structure. Cheers, Boaz. Boaz Shaanan, Ph.D. Department of Life Sciences Ben Gurion University of the Negev Beer Sheva Israel On Jun 21, 2020 00:02, Andrew Lovering <a.lover...@bham.ac.uk> wrote: Dear colleagues, I have a structure of a simple, common fold (hth, dna-binding) that I believe has oligomerized in a different way to that observed for any members of the superfamily that I can reasonably analyze. So if I run fold comparison analysis (e.g. DALI) it will find similar structures on the monomeric level but what I really want is it to find hth structures that place each monomer in a similar position to the monomers of our tetramer.....this seems harder to do [literature searches are slow and all yield tetramers dissimilar in nature to ours] I can of course "cheat" and turn our tetramer into a monomer (e.g. give the four chains the same chain ID but different residue ranges) but in something like DALI this would only get a hit to anything approximating the tetramer with a single chain protein? (I tried, this seems to be so) I hope its easier than I'm making out and would love to be enlightened! Best Andy 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