HI Armando, The “Ensemblator” (available on Github at https://github.com/Karplus-Lab-OSU/ensemblator ) is a program we published back in 2017 that aligns structures and clusters them.
Furthermore, the main purpose of the program and what I think is most unique about it, is that given two sets (clusters) of structures you are interested in, the program carries out analyses that identify the most significant structural differences both based on global overlays and in terms of local conformational differences. The paper describing the Ensemblator is: https://pubmed.ncbi.nlm.nih.gov/28762605/ HTH, Andy [Black Lives Matter] Dr. P. Andrew Karplus (he, him, his) Distinguished Professor of Biochemistry and Biophysics NIGMS GCE4All Research Center<http://gce4all.oregonstate.edu/> Director of Communications 2133 ALS Building Oregon State University Corvallis, OR 97331 ph. 541-737-3200 andy.karp...@oregonstate.edu<mailto:andy.karp...@oregonstate.edu> “Revealing how life works for the benefit of all!” http://biochem.oregonstate.edu/ https://www.facebook.com/OSUBB From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Armando Albert <xalb...@iqfr.csic.es> Date: Monday, March 6, 2023 at 7:21 AM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] Structural alignment and classification [This email originated from outside of OSU. Use caution with links and attachments.] Thank you all. What about the analysis? Does any program cluster the structures according to their structural similarity? Armando > El 6 mar 2023, a las 15:58, Harry Powell > <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> escribió: > > Hi Eleanor > > According to > > > https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ccp4.ac.uk%2Fhtml%2Fgesamt.html&data=05%7C01%7CAndy.Karplus%40oregonstate.edu%7C63abe2d2f9f14207e06f08db1e563eab%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C638137128862730618%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=3PguIbtTuxtk8mtBgna2tafOMHIbPQxF13GTjopfZOw%3D&reserved=0 > > "Gesamt aligns two or more structures…” > > and > > > https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ccp4.ac.uk%2Fhtml%2Fsuperpose.html&data=05%7C01%7CAndy.Karplus%40oregonstate.edu%7C63abe2d2f9f14207e06f08db1e563eab%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C638137128862730618%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=AH2jgosqwV%2FAK6mYaEJN4fUSYJw%2BH9NY%2BfQh9edQpfA%3D&reserved=0 > > "superpose aligns and superposes two or more protein structures…” > > But the real expert is probably Eugene. > > Harry > >> On 6 Mar 2023, at 14:55, Eleanor Dodson <eleanor.dod...@york.ac.uk> wrote: >> >> Does Superpose or GESAMT align multiple structures? >> And can either read the NMR format and apply alignment to MODEL 1 ; MODE:L 2 >> etc? >> Eleanor >> >> On Mon, 6 Mar 2023 at 14:53, Harry Powell >> <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk> wrote: >> Or you could use Gesamt - also in CCP4. >> >> Harry >> >>> On 6 Mar 2023, at 13:15, Kay Diederichs <kay.diederi...@uni-konstanz.de> >>> wrote: >>> >>> Dear Armando, >>> >>> besides THESEUS, you could use SUPERPOSE (in CCP4) or USalign >>> (https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fzhanggroup.org%2FUS-align%2F&data=05%7C01%7CAndy.Karplus%40oregonstate.edu%7C63abe2d2f9f14207e06f08db1e563eab%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C638137128862730618%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ZMl04%2B8PZVkXxpQpsEBt2bxUngxVsiBRGUhCVIOy7AE%3D&reserved=0). >>> In my tests, THESEUS sometimes crashed in different ways. USalign is very >>> robust; SUPERPOSE is fast. >>> >>> HTH, >>> Kay >>> >>> On Mon, 6 Mar 2023 08:35:20 +0100, Armando Albert <xalb...@iqfr.csic.es> >>> wrote: >>> >>>> Dear all, >>>> I want to align several structures we obtained from a fragment screening >>>> campaign and cluster them according to RMSD. >>>> Is MNYFIT still running? What else can I run? >>>> Thank you >>>> Armando >>>> >>>> ######################################################################## >>>> >>>> To unsubscribe from the CCP4BB list, click the following link: >>>> https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1&data=05%7C01%7CAndy.Karplus%40oregonstate.edu%7C63abe2d2f9f14207e06f08db1e563eab%7Cce6d05e13c5e4d6287a84c4a2713c113%7C0%7C0%7C638137128862730618%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=NYNkf1oYgiZ%2BKNrjn8LtjoeGqZMoP8uCGxhJHt3kAfQ%3D&reserved=0 >>>> >>>> This message was issued to members of >>>> 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