Thanks for the recommendations. From: Dias, Joao M. <jmd...@pfizer.com> Sent: Thursday, 2 March 2023 10:17 AM To: Joel Tyndall <joel.tynd...@otago.ac.nz>; CCP4BB@JISCMAIL.AC.UK Subject: RE: Protein models with Cofactors, metal clusters and heme
Hi Joel, Have you tried Alphafill: AlphaFold Filled (alphafill.eu)<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Falphafill.eu%2F&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7C8cf6a14d32574454456008db1a9a5287%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C638133022788484356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=JI72AhH0pyFxXYdW7yGmou3ZSUa7ftuVhVHCLFJa4eg%3D&reserved=0> https://alphafill.eu/ AlphaFill: enriching AlphaFold models with ligands and cofactors Maarten L. Hekkelman, Ida de Vries, Robbie P. Joosten & Anastassis Perrakis Nature Methods volume 20, pages205–213 (2023) https://www.nature.com/articles/s41592-022-01685-y<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41592-022-01685-y&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7C8cf6a14d32574454456008db1a9a5287%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C638133022788484356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=PxOYMNnpZMRl7IawZs6w8aK2wytbqkix3ghZ6cTrc8Q%3D&reserved=0> Good luck, Joao Joao M. Dias, Ph.D. Principal Scientist Pfizer Structural and Molecular Sciences Building 220/ room 3263, MS-8220-3224 445 Eastern Point Rd. Groton, CT 06340 From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK>> On Behalf Of Joel Tyndall Sent: Wednesday, March 1, 2023 4:10 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [EXTERNAL] [ccp4bb] Protein models with Cofactors, metal clusters and heme Hi, I have a slightly off topic question around structure models, e.g. Homology modelling. It may appear that Alpha fold etc could make homology modelling somewhat redundant. However I have noticed that in at least two structures, either a cofactor or heme are not present on the Alphafold models (that I am aware of). Is anyone aware of any webserver/package that will model these cofactors reliably (outside of modeller)? Many thanks J Joel Tyndall | BSc(Hons) PhD Professor in Medicinal Chemistry School of Pharmacy | He Rau Kawakawa University of Otago | Te Whare Wānanga o Otāgo PO Box 56 9054 Dunedin | Ōtepoti New Zealand | Aotearoa Ph: 64 3 479 7293 Website | pharmacy.otago.ac.nz<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__http%3A%2Fpharmacy.otago.ac.nz__%3B!!H9nueQsQ!-8ToqYWLFzEomDSOyXoLqbjfu9cvBGCMHVQQL7xOvV9gs9bpoPV1GEZgbVvGdJiS5UoZz1DgybeZrnr_RfC3-xPE%24&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7C8cf6a14d32574454456008db1a9a5287%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C638133022788484356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iXwzY4qUseOcnLmdde%2BBciF%2Fkich8AFgX%2FXwH3DJCh8%3D&reserved=0> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2FWA-JISC.exe%3FSUBED1%3DCCP4BB%26A%3D1__%3B!!H9nueQsQ!-8ToqYWLFzEomDSOyXoLqbjfu9cvBGCMHVQQL7xOvV9gs9bpoPV1GEZgbVvGdJiS5UoZz1DgybeZrnr_RQYnWTSP%24&data=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7C8cf6a14d32574454456008db1a9a5287%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C638133022788484356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=N1vIBoiWk%2FoIwPIx6znieQS0DRh50pbp0l1go%2FacmfA%3D&reserved=0> ######################################################################## 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/
