Thanks for the recommendations.
From: Dias, Joao M.
Sent: Thursday, 2 March 2023 10:17 AM
To: Joel Tyndall ; 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=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7C8cf6a14d32574454456008db1a9a5287%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C638133022788484356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=JI72AhH0pyFxXYdW7yGmou3ZSUa7ftuVhVHCLFJa4eg%3D=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=05%7C01%7Cjoel.tyndall%40OTAGO.AC.NZ%7C8cf6a14d32574454456008db1a9a5287%7C0225efc578fe4928b1579ef24809e9ba%7C0%7C0%7C638133022788484356%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=PxOYMNnpZMRl7IawZs6w8aK2wytbqkix3ghZ6cTrc8Q%3D=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 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 |
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