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OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
View ORCID ProfileGustaf Ahdritz, View ORCID ProfileNazim Bouatta, View ORCID ProfileSachin Kadyan, Qinghui Xia, View ORCID ProfileWilliam Gerecke, View ORCID ProfileTimothy J O’Donnell, View ORCID ProfileDaniel Berenberg, Ian Fisk, View ORCID ProfileNiccolò Zanichelli, View ORCID ProfileBo Zhang, View ORCID ProfileArkadiusz Nowaczynski, View ORCID ProfileBei Wang, View ORCID ProfileMarta M Stepniewska-Dziubinska, View ORCID ProfileShang Zhang, View ORCID ProfileAdegoke Ojewole, Murat Efe Guney, View ORCID ProfileStella Biderman, View ORCID ProfileAndrew M Watkins, View ORCID ProfileStephen Ra, View ORCID ProfilePablo Ribalta Lorenzo, Lucas Nivon, View ORCID ProfileBrian Weitzner, View ORCID ProfileYih-En Andrew Ban, View ORCID ProfilePeter K Sorger, Emad Mostaque, View ORCID ProfileZhao Zhang, View ORCID ProfileRichard Bonneau, View ORCID ProfileMohammed AlQuraishi
doi: https://doi.org/10.1101/2022.11.20.517210
Gustaf Ahdritz
1Department of Systems Biology, Columbia University
2Harvard University
Nazim Bouatta
3Laboratory of Systems Pharmacology, Harvard Medical School
Sachin Kadyan
1Department of Systems Biology, Columbia University
Qinghui Xia
1Department of Systems Biology, Columbia University
William Gerecke
3Laboratory of Systems Pharmacology, Harvard Medical School
Timothy J O’Donnell
4Icahn School of Medicine at Mount Sinai
Daniel Berenberg
5Prescient Design, Genentech
6Department of Computer Science, Courant Institute of Mathematical Sciences, New York University
Ian Fisk
7Flatiron Institute
Niccolò Zanichelli
8OpenBioML
Bo Zhang
9Scientific Computing and Imaging Institute, University of Utah
Arkadiusz Nowaczynski
10NVIDIA
Bei Wang
10NVIDIA
Marta M Stepniewska-Dziubinska
10NVIDIA
Shang Zhang
10NVIDIA
Adegoke Ojewole
10NVIDIA
Murat Efe Guney
10NVIDIA
Stella Biderman
11EleutherAI
12Booz Allen Hamilton
Andrew M Watkins
5Prescient Design, Genentech
Stephen Ra
5Prescient Design, Genentech
Pablo Ribalta Lorenzo
10NVIDIA
Lucas Nivon
13Cyrus Bio
Brian Weitzner
14Outpace Bio
Yih-En Andrew Ban
15Arzeda
Peter K Sorger
3Laboratory of Systems Pharmacology, Harvard Medical School
Emad Mostaque
16Stability AI
Zhao Zhang
17Texas Advanced Computing Center
Richard Bonneau
5Prescient Design, Genentech
Mohammed AlQuraishi
1Department of Systems Biology, Columbia University
Article usage
Posted November 22, 2022.
OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Qinghui Xia, William Gerecke, Timothy J O’Donnell, Daniel Berenberg, Ian Fisk, Niccolò Zanichelli, Bo Zhang, Arkadiusz Nowaczynski, Bei Wang, Marta M Stepniewska-Dziubinska, Shang Zhang, Adegoke Ojewole, Murat Efe Guney, Stella Biderman, Andrew M Watkins, Stephen Ra, Pablo Ribalta Lorenzo, Lucas Nivon, Brian Weitzner, Yih-En Andrew Ban, Peter K Sorger, Emad Mostaque, Zhao Zhang, Richard Bonneau, Mohammed AlQuraishi
bioRxiv 2022.11.20.517210; doi: https://doi.org/10.1101/2022.11.20.517210
OpenFold: Retraining AlphaFold2 yields new insights into its learning mechanisms and capacity for generalization
Gustaf Ahdritz, Nazim Bouatta, Sachin Kadyan, Qinghui Xia, William Gerecke, Timothy J O’Donnell, Daniel Berenberg, Ian Fisk, Niccolò Zanichelli, Bo Zhang, Arkadiusz Nowaczynski, Bei Wang, Marta M Stepniewska-Dziubinska, Shang Zhang, Adegoke Ojewole, Murat Efe Guney, Stella Biderman, Andrew M Watkins, Stephen Ra, Pablo Ribalta Lorenzo, Lucas Nivon, Brian Weitzner, Yih-En Andrew Ban, Peter K Sorger, Emad Mostaque, Zhao Zhang, Richard Bonneau, Mohammed AlQuraishi
bioRxiv 2022.11.20.517210; doi: https://doi.org/10.1101/2022.11.20.517210
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