Journal
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
Volume 116, Issue 28, Pages 13996-14001Publisher
NATL ACAD SCIENCES
DOI: 10.1073/pnas.1821905116
Keywords
deep learning; DeepEC; enzyme commission number; EC number prediction; metabolism
Categories
Funding
- Technology Development Program from the Ministry of Science and ICT through the National Research Foundation of Korea [NRF-2012M1A2A2026556, NRF-2012M1A2A2026557]
- Bio & Medical Technology Development Program of the National Research Foundation of Korea - Korean government
- Ministry of Science and ICT [NRF-2018M3A9H3020459]
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High-quality and high-throughput prediction of enzyme commission (EC) numbers is essential for accurate understanding of enzyme functions, which have many implications in pathologies and industrial biotechnology. Several EC number prediction tools are currently available, but their prediction performance needs to be further improved to precisely and efficiently process an ever-increasing volume of protein sequence data. Here, we report DeepEC, a deep learning-based computational framework that predicts EC numbers for protein sequences with high precision and in a high-throughput manner. DeepEC takes a protein sequence as input and predicts EC numbers as output. DeepEC uses 3 convolutional neural networks (CNNs) as a major engine for the prediction of EC numbers, and also implements homology analysis for EC numbers that cannot be classified by the CNNs. Comparative analyses against 5 representative EC number prediction tools show that DeepEC allows the most precise prediction of EC numbers, and is the fastest and the lightest in terms of the disk space required. Furthermore, DeepEC is the most sensitive in detecting the effects of mutated domains/binding site residues of protein sequences. DeepEC can be used as an independent tool, and also as a third-party software component in combination with other computational platforms that examine metabolic reactions.
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