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DeepVASP-E: A Flexible Analysis of Electrostatic Isopotentials for Finding and Explaining Mechanisms that Control Binding Specificity

Felix M. Quintana, Zhaoming Kong, View ORCID ProfileLifang He, View ORCID ProfileBrian Y. Chen
doi: https://doi.org/10.1101/2021.08.22.456843
Felix M. Quintana
Dept. Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
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Zhaoming Kong
Dept. Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
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Lifang He
Dept. Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
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Brian Y. Chen
Dept. Computer Science and Engineering, Lehigh University, Bethlehem, PA 18015, USA
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  • ORCID record for Brian Y. Chen
  • For correspondence: chen@cse.lehigh.edu
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Abstract

Amino acids that play a role in binding specificity can be identified with many methods, but few techniques identify the biochemical mechanisms by which they act. To address a part of this problem, we present DeepVASP-E, an algorithm that can suggest electrostatic mechanisms that influence specificity. DeepVASP-E uses convolutional neural networks to classify an electrostatic representation of ligand binding sites into specificity categories. It also uses class activation mapping to identify regions of electrostatic potential that are salient for classification. We hypothesize that electrostatic regions that are salient for classification are also likely to play a biochemical role in achieving specificity. Our findings, on two families of proteins with electrostatic influences on specificity, demonstrate that large salient regions can identify amino acids that have an electrostatic role in binding, and that DeepVASP-E is an effective classifier of ligand binding sites.

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. All rights reserved. No reuse allowed without permission.
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Posted August 23, 2021.
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DeepVASP-E: A Flexible Analysis of Electrostatic Isopotentials for Finding and Explaining Mechanisms that Control Binding Specificity
Felix M. Quintana, Zhaoming Kong, Lifang He, Brian Y. Chen
bioRxiv 2021.08.22.456843; doi: https://doi.org/10.1101/2021.08.22.456843
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DeepVASP-E: A Flexible Analysis of Electrostatic Isopotentials for Finding and Explaining Mechanisms that Control Binding Specificity
Felix M. Quintana, Zhaoming Kong, Lifang He, Brian Y. Chen
bioRxiv 2021.08.22.456843; doi: https://doi.org/10.1101/2021.08.22.456843

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