2022
DOI: 10.48550/arxiv.2202.03632
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ECRECer: Enzyme Commission Number Recommendation and Benchmarking based on Multiagent Dual-core Learning

Abstract: Enzyme Commission (EC) numbers, which associate a protein sequence with the biochemical reactions it catalyzes, are essential for the accurate understanding of enzyme functions and cellular metabolism. Many ab-initio computational approaches were proposed to predict EC numbers for given input sequences directly. However, the prediction performance (accuracy, recall, precision), usability, and efficiency of existing methods still have much room to be improved. Here, we report ECRECer, a cloud platform for accur… Show more

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“…ML methods have found invaluable applications in diverse biotechnology areas, including drug discovery (Rickerby et al, 2020), assessing various aspects of protein fitness such as thermostability (Csicsery-Ronay et al, 2022), stereoselectivity (Moon et al, 2021;Li et al, 2021), fluorescence properties (Somermeyer et al, 2022), predicting affinity in protein complex interactions (Medina-Ortiz et al, 2023;Liu et al, 2021), functional classification based on Enzyme Commission numbers (Shi et al, 2022;Fernández et al, 2023), recognition of biological activities in peptide sequences (Quiroz et al, 2021), photoreceptor adduct lifetime (Hemmer et al, 2023), and assessing DNA-binding proteins (Qu et al, 2019). The versatility of ML methods has resulted in their integration with traditional experimental techniques, such as DE and RD (Yang et al, 2019;Wittmann et al, 2021).…”
Section: Introductionmentioning
confidence: 99%
“…ML methods have found invaluable applications in diverse biotechnology areas, including drug discovery (Rickerby et al, 2020), assessing various aspects of protein fitness such as thermostability (Csicsery-Ronay et al, 2022), stereoselectivity (Moon et al, 2021;Li et al, 2021), fluorescence properties (Somermeyer et al, 2022), predicting affinity in protein complex interactions (Medina-Ortiz et al, 2023;Liu et al, 2021), functional classification based on Enzyme Commission numbers (Shi et al, 2022;Fernández et al, 2023), recognition of biological activities in peptide sequences (Quiroz et al, 2021), photoreceptor adduct lifetime (Hemmer et al, 2023), and assessing DNA-binding proteins (Qu et al, 2019). The versatility of ML methods has resulted in their integration with traditional experimental techniques, such as DE and RD (Yang et al, 2019;Wittmann et al, 2021).…”
Section: Introductionmentioning
confidence: 99%