Expanded Alphafold functionality - Try it ? Did You ? etc read up some here
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Dan Kolis
May 14, 2024, 11:22:00 AMMay 14
to DIYbio
The "Google" Alphafold had had some new functionality added. docking and tweaking whats docked, in a HTML front ended server program. Free of course, so perhaps delays for results ?
2 minute how to for WWW port:
2 minute how to for WWW port:
Anybody try this with some serious attempt to do any specific thing ? ( not just copy and paste the worked example ).
Regs
Daniel B. Kolis
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Was announced 08 May 2024 in a few forums.
Brief synopsis of announcement, at:
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Was announced 08 May 2024 in a few forums.
Brief synopsis of announcement, at:
1 12 Meg PDF has considerable detail, familiarity with nomenclatures of AF 2 would help, but is not quite required to grok this item...
TITLE:
Accurate structure prediction of biomolecular interactions with AlphaFold 3
Josh Abramson, Jonas Adler, Jack Dunger, Richard Evans, Tim Green, Alexander Pritzel, Olaf Ronneberger, Lindsay Willmore, Andrew J. Ballard, Joshua Bambrick, Sebastian W. Bodenstein, David A. Evans, Chia-Chun Hung, Michael O’Neill, David Reiman, Kathryn Tunyasuvunakool, Zachary Wu, Akvilė Žemgulytė, Eirini Arvaniti, Charles Beattie, Ottavia Bertolli, Alex Bridgland, Alexey Cherepanov, Miles Congreve, …John M. Jumper Show
Preview MTL:
We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.
Abstract
The introduction of AlphaFold XX has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design2–6. In this paper, we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture, which is capable of joint structure prediction of complexes including proteins, nucleic acids, small molecules, ions, and modified residues. The new AlphaFold model demonstrates significantly improved accuracy over many previous specialised tools: far greater accuracy on protein-ligand interactions than state of the art docking tools, much higher accuracy on protein-nucleic acid interactions than nucleic-acid-specific predictors, and significantly higher antibody-antigen prediction accuracy than AlphaFold-Multimer v2.37,8. Together these results show that high accuracy modelling across biomolecular space is possible within a single unified deep learning framework.
Preview MTL:
We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.
Abstract
The introduction of AlphaFold XX has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design2–6. In this paper, we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture, which is capable of joint structure prediction of complexes including proteins, nucleic acids, small molecules, ions, and modified residues. The new AlphaFold model demonstrates significantly improved accuracy over many previous specialised tools: far greater accuracy on protein-ligand interactions than state of the art docking tools, much higher accuracy on protein-nucleic acid interactions than nucleic-acid-specific predictors, and significantly higher antibody-antigen prediction accuracy than AlphaFold-Multimer v2.37,8. Together these results show that high accuracy modelling across biomolecular space is possible within a single unified deep learning framework.
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