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Real-Time Structure Search and Structure Classification for AlphaFold Protein Models

Tunde Aderinwale, Vijay Bharadwaj, Charles Christoffer, Genki Terashi, Zicong Zhang, Rashidedin Jahandideh, Yuki Kagaya, View ORCID ProfileDaisuke Kihara
doi: https://doi.org/10.1101/2021.10.21.465371
Tunde Aderinwale
1Department of Computer Science, Purdue University, West Lafayette, Indiana, 47907, USA
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Vijay Bharadwaj
1Department of Computer Science, Purdue University, West Lafayette, Indiana, 47907, USA
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Charles Christoffer
1Department of Computer Science, Purdue University, West Lafayette, Indiana, 47907, USA
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Genki Terashi
2Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
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Zicong Zhang
1Department of Computer Science, Purdue University, West Lafayette, Indiana, 47907, USA
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Rashidedin Jahandideh
1Department of Computer Science, Purdue University, West Lafayette, Indiana, 47907, USA
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Yuki Kagaya
2Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
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Daisuke Kihara
2Department of Biological Sciences, Purdue University, West Lafayette, Indiana, 47907, USA
1Department of Computer Science, Purdue University, West Lafayette, Indiana, 47907, USA
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  • ORCID record for Daisuke Kihara
  • For correspondence: dkihara@purdue.edu
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Abstract

AlphaFold2 showed a substantial improvement in the accuracy of protein structure prediction. Following the release of the software, whole-proteome protein structure predictions by AlphaFold2 for 21 organisms were made publicly available. Here, we developed the infrastructure, 3D-AF-Surfer, to enable real-time structure-based search for the AlphaFold2 models by combining molecular surface representation with 3D Zernike descriptors and deep neural networks.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • There was a mistake in one of the web addresses in the manuscript, and we corrected it.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted October 25, 2021.
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Real-Time Structure Search and Structure Classification for AlphaFold Protein Models
Tunde Aderinwale, Vijay Bharadwaj, Charles Christoffer, Genki Terashi, Zicong Zhang, Rashidedin Jahandideh, Yuki Kagaya, Daisuke Kihara
bioRxiv 2021.10.21.465371; doi: https://doi.org/10.1101/2021.10.21.465371
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Real-Time Structure Search and Structure Classification for AlphaFold Protein Models
Tunde Aderinwale, Vijay Bharadwaj, Charles Christoffer, Genki Terashi, Zicong Zhang, Rashidedin Jahandideh, Yuki Kagaya, Daisuke Kihara
bioRxiv 2021.10.21.465371; doi: https://doi.org/10.1101/2021.10.21.465371

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