Hi Joel, Have you tried Alphafill: AlphaFold Filled (alphafill.eu)<https://alphafill.eu/> 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 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 <[email protected]> On Behalf Of Joel Tyndall Sent: Wednesday, March 1, 2023 4:10 PM To: [email protected] 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://urldefense.com/v3/__http:/pharmacy.otago.ac.nz__;!!H9nueQsQ!-8ToqYWLFzEomDSOyXoLqbjfu9cvBGCMHVQQL7xOvV9gs9bpoPV1GEZgbVvGdJiS5UoZz1DgybeZrnr_RfC3-xPE$> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.com/v3/__https:/www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1__;!!H9nueQsQ!-8ToqYWLFzEomDSOyXoLqbjfu9cvBGCMHVQQL7xOvV9gs9bpoPV1GEZgbVvGdJiS5UoZz1DgybeZrnr_RQYnWTSP$> ######################################################################## 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/
