DORA-XGB: an improved enzymatic reaction feasibility classifier trained using a novel synthetic data approach

Chainani, Yash; Ni, Zhuofu; Shebek, Kevin M.; Broadbelt, Linda J.; Tyo, Keith E. J.

doi:10.1039/D4ME00118D

Title: DORA-XGB: an improved enzymatic reaction feasibility classifier trained using a novel synthetic data approach

Journal Article · 02 February 2025 · Molecular Systems Design & Engineering

DOI: https://doi.org/10.1039/D4ME00118D · OSTI ID:2480755

Chainani, Yash ^[1]; Ni, Zhuofu ^[1]; Shebek, Kevin M. ^[1];

^[1]; Tyo, Keith E. J. ^[1]

Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA, Center for Synthetic Biology, Northwestern University, Evanston, IL, USA

We outline a method for synthetically generating negative data by considering alternative reaction centers on small-molecule substrates that are known to participate in enzymatic reactions.

View Journal Article

Cite

Export

Save

Sponsoring Organization:: USDOE

Grant/Contract Number:: NONE; SC0018249; AC02-05CH11231

OSTI ID:: 2480755

Journal Information:: Molecular Systems Design & Engineering, Journal Name: Molecular Systems Design & Engineering Journal Issue: 2 Vol. 10; ISSN MSDEBG; ISSN 2058-9689

Publisher:: Royal Society of Chemistry (RSC)Copyright Statement

Country of Publication:: United Kingdom

Language:: English

References (53)

Expanding Metabolic Capabilities Using Novel Pathway Designs: Computational Tools and Case Studies Saa, Pedro A.; Cortés, María P.; López, Javiera Biotechnology Journal, Vol. 14, Issue 9 https://doi.org/10.1002/biot.201800734	journal	July 2019
A deep learning approach to evaluate the feasibility of enzymatic reactions generated by retrobiosynthesis Kim, Yeji; Ryu, Jae Yong; Kim, Hyun Uk Biotechnology Journal, Vol. 16, Issue 5 https://doi.org/10.1002/biot.202000605	journal	January 2021
Exploring De Novo metabolic pathways from pyruvate to propionic acid Stine, Andrew; Zhang, Miaomin; Ro, Soo Biotechnology Progress, Vol. 32, Issue 2 https://doi.org/10.1002/btpr.2233	journal	March 2016
Neural-Symbolic Machine Learning for Retrosynthesis and Reaction Prediction Segler, Marwin H. S.; Waller, Mark P. Chemistry - A European Journal, Vol. 23, Issue 25 https://doi.org/10.1002/chem.201605499	journal	February 2017
Graph Neural Networks for Molecules Wang, Yuyang; Li, Zijie; Barati Farimani, Amir Challenges and Advances in Computational Chemistry and Physics, p. 21-66 https://doi.org/10.1007/978-3-031-37196-7_2	book	October 2023
Network representation and analysis of energy coupling mechanisms in cellular metabolism by a graph-theoretical approach Nath, Sunil Theory in Biosciences, Vol. 141, Issue 3 https://doi.org/10.1007/s12064-022-00370-0	journal	May 2022
Automatic tuning of hyperparameters using Bayesian optimization Victoria, A. Helen; Maragatham, G. Evolving Systems, Vol. 12, Issue 1 https://doi.org/10.1007/s12530-020-09345-2	journal	May 2020
Channeling in native microbial pathways: Implications and challenges for metabolic engineering Abernathy, Mary H.; He, Lian; Tang, Yinjie J. Biotechnology Advances, Vol. 35, Issue 6 https://doi.org/10.1016/j.biotechadv.2017.06.004	journal	November 2017
Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways Hadadi, Noushin; Hatzimanikatis, Vassily Current Opinion in Chemical Biology, Vol. 28 https://doi.org/10.1016/j.cbpa.2015.06.025	journal	October 2015
Coal resources under carbon peak: Segmentation of massive laser point clouds for coal mining in underground dusty environments using integrated graph deep learning model Xing, Zhizhong; Zhao, Shuanfeng; Guo, Wei Energy, Vol. 285 https://doi.org/10.1016/j.energy.2023.128771	journal	December 2023
The BRENDA enzyme information system–From a database to an expert system Schomburg, I.; Jeske, L.; Ulbrich, M. Journal of Biotechnology, Vol. 261 https://doi.org/10.1016/j.jbiotec.2017.04.020	journal	November 2017
Toward the energy efficiency of resource allocation algorithms for OFDMA downlink MIMO systems Wu, Wei-Chiang Journal of Electronic Science and Technology, Vol. 17, Issue 4 https://doi.org/10.1016/j.jnlest.2020.100007	journal	December 2019
Metabolic channeling: predictions, deductions, and evidence Pareek, Vidhi; Sha, Zhou; He, Jingxuan Molecular Cell, Vol. 81, Issue 18 https://doi.org/10.1016/j.molcel.2021.08.030	journal	September 2021
Metabolon formation and metabolic channeling in the biosynthesis of plant natural products Jørgensen, Kirsten; Rasmussen, Anne Vinther; Morant, Marc Current Opinion in Plant Biology, Vol. 8, Issue 3 https://doi.org/10.1016/j.pbi.2005.03.014	journal	June 2005
Metabolic networks: enzyme function and metabolite structure Hatzimanikatis, Vassily; Li, Chunhui; Ionita, Justin A. Current Opinion in Structural Biology, Vol. 14, Issue 3 https://doi.org/10.1016/j.sbi.2004.04.004	journal	June 2004
Application of message passing neural networks for molecular property prediction Tang, Miru; Li, Baiqing; Chen, Hongming Current Opinion in Structural Biology, Vol. 81 https://doi.org/10.1016/j.sbi.2023.102616	journal	August 2023
Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path Campodonico, Miguel A.; Andrews, Barbara A.; Asenjo, Juan A. Metabolic Engineering, Vol. 25 https://doi.org/10.1016/j.ymben.2014.07.009	journal	September 2014
RetroPath2.0: A retrosynthesis workflow for metabolic engineers Delépine, Baudoin; Duigou, Thomas; Carbonell, Pablo Metabolic Engineering, Vol. 45 https://doi.org/10.1016/j.ymben.2017.12.002	journal	January 2018
Curating a comprehensive set of enzymatic reaction rules for efficient novel biosynthetic pathway design Ni, Zhuofu; Stine, Andrew E.; Tyo, Keith E. J. Metabolic Engineering, Vol. 65 https://doi.org/10.1016/j.ymben.2021.02.006	journal	May 2021
The Generation of a Unique Machine Description for Chemical Structures-A Technique Developed at Chemical Abstracts Service. Morgan, H. L. Journal of Chemical Documentation, Vol. 5, Issue 2 https://doi.org/10.1021/c160017a018	journal	May 1965
Atom pairs as molecular features in structure-activity studies: definition and applications Carhart, Raymond E.; Smith, Dennis H.; Venkataraghavan, R. Journal of Chemical Information and Modeling, Vol. 25, Issue 2 https://doi.org/10.1021/ci00046a002	journal	May 1985
Reoptimization of MDL Keys for Use in Drug Discovery Durant, Joseph L.; Leland, Burton A.; Henry, Douglas R. Journal of Chemical Information and Computer Sciences, Vol. 42, Issue 6 https://doi.org/10.1021/ci010132r	journal	November 2002
Extended-Connectivity Fingerprints Rogers, David; Hahn, Mathew Journal of Chemical Information and Modeling, Vol. 50, Issue 5 https://doi.org/10.1021/ci100050t	journal	April 2010
Retropath: Automated Pipeline for Embedded Metabolic Circuits Carbonell, Pablo; Parutto, Pierre; Baudier, Claire ACS Synthetic Biology, Vol. 3, Issue 8 https://doi.org/10.1021/sb4001273	journal	October 2013
Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli Bennett, Bryson D.; Kimball, Elizabeth H.; Gao, Melissa Nature Chemical Biology, Vol. 5, Issue 8 https://doi.org/10.1038/nchembio.186	journal	June 2009
Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli Sévin, Daniel C.; Fuhrer, Tobias; Zamboni, Nicola Nature Methods, Vol. 14, Issue 2 https://doi.org/10.1038/nmeth.4103	journal	December 2016
Pathway design using de novo steps through uncharted biochemical spaces Kumar, Akhil; Wang, Lin; Ng, Chiam Yu Nature Communications, Vol. 9, Issue 1 https://doi.org/10.1038/s41467-017-02362-x	journal	January 2018
A comprehensive metabolic map for production of bio-based chemicals Lee, Sang Yup; Kim, Hyun Uk; Chae, Tong Un Nature Catalysis, Vol. 2, Issue 1 https://doi.org/10.1038/s41929-018-0212-4	journal	January 2019
Principles and functions of metabolic compartmentalization Bar-Peled, Liron; Kory, Nora Nature Metabolism, Vol. 4, Issue 10 https://doi.org/10.1038/s42255-022-00645-2	journal	October 2022
Enzyme promiscuity prediction using hierarchy-informed multi-label classification Visani, Gian Marco; Hughes, Michael C.; Hassoun, Soha Bioinformatics, Vol. 37, Issue 14 https://doi.org/10.1093/bioinformatics/btab054	journal	January 2021
eQuilibrator 3.0: a database solution for thermodynamic constant estimation Beber, Moritz E.; Gollub, Mattia G.; Mozaffari, Dana Nucleic Acids Research, Vol. 50, Issue D1 https://doi.org/10.1093/nar/gkab1106	journal	November 2021
KEGG: new perspectives on genomes, pathways, diseases and drugs Kanehisa, Minoru; Furumichi, Miho; Tanabe, Mao Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1092	journal	November 2016
RetroRules: a database of reaction rules for engineering biology Duigou, Thomas; du Lac, Melchior; Carbonell, Pablo Nucleic Acids Research, Vol. 47, Issue D1 https://doi.org/10.1093/nar/gky940	journal	October 2018
The MetaCyc database of metabolic pathways and enzymes - a 2019 update Caspi, Ron; Billington, Richard; Keseler, Ingrid M. Nucleic Acids Research, Vol. 48, Issue D1 https://doi.org/10.1093/nar/gkz862	journal	October 2019
Energy coupling in Saccharomyces cerevisiae: selected opportunities for metabolic engineering Kok, Stefan; Kozak, Barbara U.; Pronk, Jack T. FEMS Yeast Research, Vol. 12, Issue 4 https://doi.org/10.1111/j.1567-1364.2012.00799.x	journal	April 2012
Manufacturing Molecules Through Metabolic Engineering Keasling, Jay D. Science, Vol. 330, Issue 6009, p. 1355-1358 https://doi.org/10.1126/science.1193990	journal	December 2010
Evolutionary-scale prediction of atomic-level protein structure with a language model Lin, Zeming; Akin, Halil; Rao, Roshan Science, Vol. 379, Issue 6637 https://doi.org/10.1126/science.ade2574	journal	March 2023
Enzyme function prediction using contrastive learning Yu, Tianhao; Cui, Haiyang; Li, Jianan Canal Science, Vol. 379, Issue 6639 https://doi.org/10.1126/science.adf2465	journal	March 2023
The EcoCyc Database Karp, Peter D.; Ong, Wai Kit; Paley, Suzanne EcoSal Plus, Vol. 8, Issue 1 https://doi.org/10.1128/ecosalplus.esp-0006-2018	journal	February 2018
XGBoost: A Scalable Tree Boosting System Chen, Tianqi; Guestrin, Carlos Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining - KDD '16 https://doi.org/10.1145/2939672.2939785	conference	January 2016
Bias in machine learning software: why? how? what to do? Chakraborty, Joymallya; Majumder, Suvodeep; Menzies, Tim Proceedings of the 29th ACM Joint Meeting on European Software Engineering Conference and Symposium on the Foundations of Software Engineering https://doi.org/10.1145/3468264.3468537	conference	August 2021
Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation Fackler, Nick; Heijstra, Björn D.; Rasor, Blake J. Annual Review of Chemical and Biomolecular Engineering, Vol. 12, Issue 1 https://doi.org/10.1146/annurev-chembioeng-120120-021122	journal	June 2021
The influence of negative training set size on machine learning-based virtual screening Kurczab, Rafał; Smusz, Sabina; Bojarski, Andrzej J. Journal of Cheminformatics, Vol. 6, Issue 1 https://doi.org/10.1186/1758-2946-6-32	journal	June 2014
Pickaxe: a Python library for the prediction of novel metabolic reactions Shebek, Kevin M.; Strutz, Jonathan; Broadbelt, Linda J. BMC Bioinformatics, Vol. 24, Issue 1 https://doi.org/10.1186/s12859-023-05149-8	journal	March 2023
MINEs: open access databases of computationally predicted enzyme promiscuity products for untargeted metabolomics Jeffryes, James G.; Colastani, Ricardo L.; Elbadawi-Sidhu, Mona Journal of Cheminformatics, Vol. 7, Issue 1 https://doi.org/10.1186/s13321-015-0087-1	journal	August 2015
Mordred: a molecular descriptor calculator Moriwaki, Hirotomo; Tian, Yu-Shi; Kawashita, Norihito Journal of Cheminformatics, Vol. 10, Issue 1 https://doi.org/10.1186/s13321-018-0258-y	journal	February 2018
Automated reaction database and reaction network analysis: extraction of reaction templates using cheminformatics Plehiers, Pieter P.; Marin, Guy B.; Stevens, Christian V. Journal of Cheminformatics, Vol. 10, Issue 1 https://doi.org/10.1186/s13321-018-0269-8	journal	March 2018
One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome Capecchi, Alice; Probst, Daniel; Reymond, Jean-Louis Journal of Cheminformatics, Vol. 12, Issue 1 https://doi.org/10.1186/s13321-020-00445-4	journal	June 2020
Could graph neural networks learn better molecular representation for drug discovery? A comparison study of descriptor-based and graph-based models Jiang, Dejun; Wu, Zhenxing; Hsieh, Chang-Yu Journal of Cheminformatics, Vol. 13, Issue 1 https://doi.org/10.1186/s13321-020-00479-8	journal	February 2021
Pathway Thermodynamics Highlights Kinetic Obstacles in Central Metabolism Noor, Elad; Bar-Even, Arren; Flamholz, Avi PLoS Computational Biology, Vol. 10, Issue 2 https://doi.org/10.1371/journal.pcbi.1003483	journal	February 2014
Predictive classifier models built from natural products with antimalarial bioactivity using machine learning approach Egieyeh, Samuel; Syce, James; Malan, Sarel F. PLOS ONE, Vol. 13, Issue 9 https://doi.org/10.1371/journal.pone.0204644	journal	September 2018
An empirical evaluation of sampling methods for the classification of imbalanced data Kim, Misuk; Hwang, Kyu-Baek PLOS ONE, Vol. 17, Issue 7 https://doi.org/10.1371/journal.pone.0271260	journal	July 2022
SMOTE: Synthetic Minority Over-sampling Technique Chawla, N. V.; Bowyer, K. W.; Hall, L. O. Journal of Artificial Intelligence Research, Vol. 16 https://doi.org/10.1613/jair.953	journal	January 2002

Similar Records

Curating a comprehensive set of enzymatic reaction rules for efficient novel biosynthetic pathway design

Journal Article · 2021 · Metabolic Engineering · OSTI ID:1852562

Ni, Zhuofu; Stine, Andrew E.; Tyo, Keith E. J.; +1 more

Agents for replacement of NAD+/NADH system in enzymatic reactions

Patent · 2004 · OSTI ID:1174800

Fish, Richard H.; Kerr, John B.; Lo, Christine H.

Placing Single-Molecule T4 Lysozyme Enzymes on a Bacterial Cell Surface: Toward Probing Single-Molecule Enzymatic Reaction in Living Cells

Journal Article · 2004 · Biophysical Journal · OSTI ID:15008811

Hu, Dehong; Lu, H PETER

Title: DORA-XGB: an improved enzymatic reaction feasibility classifier trained using a novel synthetic data approach

Citation Formats

References (53)

Similar Records

Related Subjects