Journal
FRONTIERS IN MICROBIOLOGY
Volume 12, Issue -, Pages -Publisher
FRONTIERS MEDIA SA
DOI: 10.3389/fmicb.2021.725727
Keywords
antimicrobial peptides; minimum inhibitory concentration; generative deep learning; activity prediction; variational autoencoder
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Funding
- Jerome and Isabella Karle Distinguished Scholar Fellowship by the Naval Research Laboratory, base funds of the Naval Research Laboratory [1V33]
- Defense Threat Reduction Agency [HDTRA1033536]
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The study introduces the PepVAE framework for designing novel AMPs using VAE and antimicrobial activity prediction models. By sampling from different regions of the learned latent space, new AMP sequences can be generated with minimal input parameters for controlled production of AMPs with predicted antimicrobial activity. This modular design framework shows promise for development of novel AMPs with experimental validation.
New methods for antimicrobial design are critical for combating pathogenic bacteria in the post-antibiotic era. Fortunately, competition within complex communities has led to the natural evolution of antimicrobial peptide (AMP) sequences that have promising bactericidal properties. Unfortunately, the identification, characterization, and production of AMPs can prove complex and time consuming. Here, we report a peptide generation framework, PepVAE, based around variational autoencoder (VAE) and antimicrobial activity prediction models for designing novel AMPs using only sequences and experimental minimum inhibitory concentration (MIC) data as input. Sampling from distinct regions of the learned latent space allows for controllable generation of new AMP sequences with minimal input parameters. Extensive analysis of the PepVAE-generated sequences paired with antimicrobial activity prediction models supports this modular design framework as a promising system for development of novel AMPs, demonstrating controlled production of AMPs with experimental validation of predicted antimicrobial activity.
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