Re: [ccp4bb] Thanks and outcome of ([ccp4bb] Looking for method to find similar oligomeric arrangement)

A further note on assembly search: since April the RCSB PDB offers structure search for assemblies. See the "Structure Similarity" section in https://www.rcsb.org/search/advanced. This works only for PDB-deposited structures but we are working on making it available for 3D coordinates submitted by

[ccp4bb] Thanks and outcome of ([ccp4bb] Looking for method to find similar oligomeric arrangement)

Dear All Many thanks to Johann for the suggestion of Topsearch - rather pleasingly our tetramer is novel in the tetrameric arrangement, but each of the dimers has its DNA recognition helices in agreement with several hits a win all round Bringing joy to my lockdown. Best Andy

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

at, https://topsearch.services.came.sbg.ac.at/ > > Best, > > Hans > > > > *Von:* CCP4 bulletin board *Im Auftrag von *Andrew > Lovering > *Gesendet:* Sonntag, 21. Juni 2020 10:51 > *An:* CCP4BB@JISCMAIL.AC.UK > *Betreff:* Re: [ccp4bb] Looking for method to find si

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

Topsearch does that, https://topsearch.services.came.sbg.ac.at/ Best, Hans Von: CCP4 bulletin board Im Auftrag von Andrew Lovering Gesendet: Sonntag, 21. Juni 2020 10:51 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] Looking for method to find similar oligomeric arrangement Thanks Boaz

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

Thanks to all of you pointing me towards ProtCID, but unless I'm mistaken this works only for deposited co-ordinates / PDB entries? I was more looking for something that would take my (yet to be deposited) PDB file, with its inherent tetrametric hth fold, and find similar folds in similar

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

Hi Andy, Are you familiar with ProtCID? http://dunbrack2.fccc.edu/ProtCiD/Default.aspx Might be relevant. Best, Orly On Sun, Jun 21, 2020 at 12:02 AM Andrew Lovering wrote: > Dear colleagues, > > > I have a structure of a simple, common fold (hth, dna-binding) that I > believe has

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

Thanks Boaz for the SSM heads up. I was much too DALI-centric! One last point, if anyone can offer an opinion - I presume most methods will match but only within ASU contents. Does any approach utilize deposited "biological unit" classification or (better still) crystallographic symmetry

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

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

[ccp4bb] Looking for method to find similar oligomeric arrangement

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