Cited by 551Computational Drug Discovery MethodsMicrobial Natural Products and BiosynthesisMachine Learning in Materials Science

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NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products

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Kim, Hyun Woo, Wang, Mingxun, Leber, Christopher A., Nothias, Louis-Félix, Reher, Raphael, Kang, Kyo Bin, van der Hooft, Justin J. J., Dorrestein, Pieter C., Gerwick, William H., Cottrell, Garrison W.·2021·Journal of Natural Products

DOI 10.1021/acs.jnatprod.1c00399PMC PMC8631337

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Abstract

Computational approaches such as genome and metabolome mining are becoming essential to natural products (NPs) research. Consequently, a need exists for an automated structure-type classification system to handle the massive amounts of data appearing for NP structures. An ideal semantic ontology for the classification of NPs should go beyond the simple presence/absence of chemical substructures, but also include the taxonomy of the producing organism, the nature of the biosynthetic pathway, and/or their biological properties. Thus, a holistic and automatic NP classification framework could have considerable value to comprehensively navigate the relatedness of NPs, and especially so when analyzing large numbers of NPs. Here, we introduce NPClassifier, a deep-learning tool for the automated structural classification of NPs from their counted Morgan fingerprints. NPClassifier is expected to accelerate and enhance NP discovery by linking NP structures to their underlying properties.

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Authors: Kim, H. W., Wang, M., Leber, C. A., Nothias, L.-F., Reher, R., Kang, K. B., van der Hooft, J. J. J., Dorrestein, P. C., Gerwick, W. H., & Cottrell, G. W.
Affiliations: Scripps Institution of Oceanography (US)
University of California San Diego (US)
Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, La Jolla, California 92093, United States
Sookmyung Women's University (KR)
Bioinformatics Group, Wageningen University, Wageningen 6700, The Netherlands
Corresponding author: Gerwick, William H.
Cottrell, Garrison W.
ORCID: Kim, Hyun Woo
Wang, Mingxun
Leber, Christopher A.
Reher, Raphael
Kang, Kyo Bin
van der Hooft, Justin J. J.
Dorrestein, Pieter C.
Gerwick, William H.
Cottrell, Garrison W.
Venue: Journal of Natural Products
Publisher: American Chemical Society (ACS)
Published: 2021-10-18
Volume: 84
Issue: 11
Pages: 2795-2807
ISSN: 0163-3864 (ISSN-L)
1520-6025
DOI: 10.1021/acs.jnatprod.1c00399
PMC: PMC8631337
OpenAlex: W3206742358
Cited by: 551
References: 70
Citations by year: 2026: 140 · 2025: 165 · 2024: 115 · 2023: 83 · 2022: 30 · 2021: 18
FWCI: 32.17
Type: journal article
Language: en
Open access: hybrid
doi.org
Licence: cc-by-nc-nd
creativecommons.org/licenses/by-nc-nd/4.0/ (unspecified)
Locations: Journal of Natural Products (publishedVersion, cc-by-nc-nd)
ChemRxiv (acceptedVersion, cc-by-nc-nd)
PubMed Central (publishedVersion, cc-by-nc-nd)
PubMed (publishedVersion)
Socio-Environmental Systems Modeling (acceptedVersion, cc-by-nc-nd)
eScholarship (California Digital Library) (submittedVersion, cc-by-nc-nd)
Figshare (submittedVersion)
Zenodo (CERN European Organization for Nuclear Research) (submittedVersion, cc-by)
Data Archiving and Networked Services (DANS) (submittedVersion, cc-by-nc-nd)
Funders: Gordon and Betty Moore Foundation (GBMF7622)
National Research Foundation of Korea (NRF-2020R1C1C1004046)
Netherlands eScience Center (ASDI.2017.030)
National Institute of General Medical Sciences (R01 GM107550)
Topics: Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
Life Sciences › Immunology and Microbiology › Applied Microbiology and Biotechnology › Microbial Natural Products and Biosynthesis
Physical Sciences › Materials Science › Materials Chemistry › Machine Learning in Materials Science
Keywords: natural products, structural classification, Morgan fingerprints, deep neural network, natural product discovery, biosynthetic pathway, chemical substructures
MeSH terms: Biological Products, Neural Networks, Computer, Biosynthetic Pathways

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NPClassifier: A Deep Neural Network-Based Structural Classification Tool for Natural Products

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