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Model Details
Domain:
Task:
Model Access:
Open weights (non-commercial)
Introduction
The introduction of AlphaFold 2 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design Here we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture that is capable of predicting the joint structure of complexes including proteins, nucleic acids, small molecules, ions and modified residues. The new AlphaFold model demonstrates substantially improved accuracy over many previous specialized tools: far greater accuracy for protein–ligand interactions compared with state-of-the-art docking tools, much higher accuracy for protein–nucleic acid interactions compared with nucleic-acid-specific predictors and substantially higher antibody–antigen prediction accuracy compared with AlphaFold-Multimer. Together, these results show that high-accuracy modelling across biomolecular space is possible within a single unified deep-learning framework.
Benchmarking
FLOPs4.14e+22
Notes: 256 GPUs * 480 hours [see training time notes] * 3600 sec / hour * 312000000000000 FLOP / GPU / sec * 0.3 [assumed utilization] = 4.1405645e+22 FLOP
Training
Training Code AccessibilityInference code CC-BY-NC-SA 4.0 weights - permissions given after approval (only non-commercial use) "AlphaFold 3 will be available as a non-commercial usage only server at https://www.alphafoldserver.com, with restrictions on allowed ligands and covalent modifications. Pseudocode describing the algorithms is available in the Supplementary Information. Code is not provided"
HardwareNVIDIA A100
Hardware Quantity256
Size Notes: from https://www.biorxiv.org/content/10.1101/2024.11.19.624167v2.full.pdf "As a comparison AlphaFol3 trained a similar architecture for nearly 150k steps with a batch size of 256" from supplementary materials "The model is trained with a batch size of 256" 150000 steps * 256 sequences per batch * 384 tokens per batch [at initial training stage, Table 6, supplementary materials] = 14 745 600 000 tokens from supplementary materials Table 6 fine-tuning took exactly the same amount of GPU-hours -> the entire amount of training tokens is 14 745 600 000 * 2 = 29491200000
Authors
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, Alexander I. Cowen-Rivers, Andrew Cowie, Michael Figurnov, Fabian B. Fuchs, Hannah Gladman, Rishub Jain, Yousuf A. Khan, Caroline M. R. Low, Kuba Perlin, Anna Potapenko, Pascal Savy, Sukhdeep Singh, Adrian Stecula, Ashok Thillaisundaram, Catherine Tong, Sergei Yakneen, Ellen D. Zhong, Michal Zielinski, Augustin Žídek, Victor Bapst, Pushmeet Kohli, Max Jaderberg, Demis Hassabis, John M. Jumper
Multimodal
Language
Vision
Video
Speech