id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 15135 AlphaFold3 and ChimeraX okovalevskiy@… Tom Goddard "{{{ Dear ChimeraX team, I hope you are keeping well. I would like to take this opportunity to thank you for all the great work on supporting AlphaFold2 in the ChimeraX and implementing excellent visualisation of the confidence metrics like your integrated PAE viewer. As the key community members, I wanted to share an exciting announcement . Today, Google DeepMind announced AlphaFold 3 via a paper in Nature. AlphaFold 3 is the next generation of AlphaFold, developed by Google Deepmind and Isomorphic Labs, which can predict the structures of nearly every biomolecule type — with state-of-the-art accuracy. We have two main pieces of news to share: 1) Where previously AlphaFold predicted the 3D structures of proteins, AlphaFold 3 can model other biomolecules, including DNA, RNA, ligands, and ions, model large, complex structures made of these biomolecules, and predict biologically meaningful interactions between them. Which we hope will unlock significant further research directions across the life sciences. If you would like to read more about the model’s new capabilities please see the paper in Nature. 2) Alongside this, we are launching AlphaFold Server . Powered by AlphaFold 3, the Server is an easy to use, web-based tool for non-commercial researchers to access AlphaFold 3’s predictions for non-commercial research. AlphaFold Server makes the majority of AlphaFold 3 capabilities available- with the exception of some biomolecule capabilities, particularly those relevant to drug discovery. It will be the most accurate tool for predicting how proteins interact with the other molecular components of the cell. The server is free of charge for users, which we hope will enable even more researchers to make use of structures as they build their understanding of the processes underpinning the living world. Please note that the AlphaFold Server also produces JSON files carrying PAE (they are available as part of zip file for download). However, our new implementation may not be compatible with ChimeraX visualisation of the PAE plot. The reason is that PAE plot for AlphaFold2 was based on amino acid residues, and for AlphaFold3 PAE is based on tokens (one token per standard amino acid residue or nucleotide, one token per atom of any chemically modified residue, nucleotide, ligand or ion). I am absolutely happy to discuss this difference in more detail; we can set up a video chat, if you are interested. We are excited to share this news with you, and welcome any feedback you might have on this announcement or AlphaFold Server more broadly. Please also feel free to share this with your colleagues and wider network. All the best, Oleg -- [image: logo] Oleg Kovalevskiy Applied Scientist okovalevskiy@deepmind.com If you received this email in error, please do not forward it to anyone else (it may contain confidential or privileged information), erase all copies and attachments, and let me know that it has gone to the wrong person. }}} " task closed normal Structure Prediction fixed Scooter Morris all ChimeraX