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Predicting Antibody Developability from Sequence using Machine Learning

Xingyao Chen, Thomas Dougherty, Chan Hong, Rachel Schibler, Yi Cong Zhao, Reza Sadeghi, Naim Matasci, Yi-Chieh Wu, Ian Kerman
doi: https://doi.org/10.1101/2020.06.18.159798
Xingyao Chen
1Department of Computer Science, Harvey Mudd College, Claremont, California, USA
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Thomas Dougherty
1Department of Computer Science, Harvey Mudd College, Claremont, California, USA
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Chan Hong
1Department of Computer Science, Harvey Mudd College, Claremont, California, USA
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Rachel Schibler
1Department of Computer Science, Harvey Mudd College, Claremont, California, USA
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Yi Cong Zhao
1Department of Computer Science, Harvey Mudd College, Claremont, California, USA
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Reza Sadeghi
2Dassault Systèmes BIOVIA, San Diego, California, USA
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Naim Matasci
3Department of Biology, Harvey Mudd College, Claremont, California, USA
4Lawrence J. Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, California, USA
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Yi-Chieh Wu
1Department of Computer Science, Harvey Mudd College, Claremont, California, USA
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  • For correspondence: yjw@cs.hmc.edu
Ian Kerman
2Dassault Systèmes BIOVIA, San Diego, California, USA
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Abstract

Antibodies are prominent therapeutic agents but costly to develop. Existing approaches to predict developability depend on structure, which requires expensive laboratory or computational work to obtain. To address this issue, we present a machine learning pipeline to predict developability from sequence alone using physicochemical and learned embedding features. Our approach achieves high sensitivity and specificity on a dataset of 2400 antibodies. These results suggest that sequence is predictive of developability, enabling more efficient development of antibodies.

Competing Interest Statement

The authors have declared no competing interest.

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 June 20, 2020.
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Predicting Antibody Developability from Sequence using Machine Learning
Xingyao Chen, Thomas Dougherty, Chan Hong, Rachel Schibler, Yi Cong Zhao, Reza Sadeghi, Naim Matasci, Yi-Chieh Wu, Ian Kerman
bioRxiv 2020.06.18.159798; doi: https://doi.org/10.1101/2020.06.18.159798
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Predicting Antibody Developability from Sequence using Machine Learning
Xingyao Chen, Thomas Dougherty, Chan Hong, Rachel Schibler, Yi Cong Zhao, Reza Sadeghi, Naim Matasci, Yi-Chieh Wu, Ian Kerman
bioRxiv 2020.06.18.159798; doi: https://doi.org/10.1101/2020.06.18.159798

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