메뉴 건너뛰기




Volumn 14, Issue , 2019, Pages 82-107

Retrosynthetic design of metabolic pathways to chemicals not found in nature

Author keywords

Artificial intelligence; Machine learning; Synthetic biology; Systems biology

Indexed keywords

ARTIFICIAL INTELLIGENCE; CHEMISTRY; CONSUMER; HUMAN; MACHINE LEARNING; METABOLISM; REVIEW; SYNTHETIC BIOLOGY; SYSTEMS BIOLOGY;

EID: 85067169925     PISSN: None     EISSN: 24523100     Source Type: Journal    
DOI: 10.1016/j.coisb.2019.04.004     Document Type: Review
Times cited : (102)

References (352)
  • 1
    • 0011362257 scopus 로고
    • General methods for the construction of complex molecules
    • Corey, E.J., General methods for the construction of complex molecules. Pure Appl Chem 14 (1967), 19–37.
    • (1967) Pure Appl Chem , vol.14 , pp. 19-37
    • Corey, E.J.1
  • 3
    • 0004220870 scopus 로고    scopus 로고
    • Classics in total synthesis: targets, strategies, methods
    • Wiley-VCH
    • Nicolaou, K.C., Sorensen, E.J., Classics in total synthesis: targets, strategies, methods. 1996, Wiley-VCH.
    • (1996)
    • Nicolaou, K.C.1    Sorensen, E.J.2
  • 4
    • 0042261072 scopus 로고    scopus 로고
    • Classics in total synthesis II: more targets, strategies, methods
    • Wiley-VCH
    • Nicolaou, K.C., Snyder, S.A., Classics in total synthesis II: more targets, strategies, methods. 2003, Wiley-VCH.
    • (2003)
    • Nicolaou, K.C.1    Snyder, S.A.2
  • 5
    • 0042261072 scopus 로고    scopus 로고
    • Classics in total synthesis III: further targets, strategies, methods
    • Wiley-VCH
    • Nicolaou, K.C., Chen, J.S., Classics in total synthesis III: further targets, strategies, methods. 2011, Wiley-VCH.
    • (2011)
    • Nicolaou, K.C.1    Chen, J.S.2
  • 6
    • 84981765197 scopus 로고    scopus 로고
    • Computer-Assisted synthetic planning: the end of the beginning
    • The paper provides an in-depth overview of the algorithm Chematica uses to navigate through the network of organic chemistry. It also discusses the human-curated rules in Chematica and their use for de novo retrosynthetic design.
    • Nicolaou KC, Chen JS: Classics in total synthesis III: further targets, strategies, methods. Wiley-VCH; 2011.
    • (2016) Angew Chem Int Ed , vol.55 , pp. 5904-5937
    • Szymkuć, S.1    Gajewska, E.P.2    Klucznik, T.3    Molga, K.4    Dittwald, P.5    Startek, M.6    Bajczyk, M.7    Grzybowski, B.A.8
  • 8
    • 84942013003 scopus 로고    scopus 로고
    • A highly characterized yeast toolkit for modular, multipart assembly
    • Lee, M.E., DeLoache, W.C., Cervantes, B., Dueber, J.E., A highly characterized yeast toolkit for modular, multipart assembly. ACS Synth Biol 4 (2015), 975–986.
    • (2015) ACS Synth Biol , vol.4 , pp. 975-986
    • Lee, M.E.1    DeLoache, W.C.2    Cervantes, B.3    Dueber, J.E.4
  • 9
    • 85047558331 scopus 로고    scopus 로고
    • Iterative algorithm-guided design of massive strain libraries, applied to itaconic acid production in yeast
    • Young, E.M., Zhao, Z., Gielesen, B.E.M., Wu, L., Benjamin Gordon, D., Roubos, J.A., Voigt, C.A., Iterative algorithm-guided design of massive strain libraries, applied to itaconic acid production in yeast. Metab Eng 48 (2018), 33–43.
    • (2018) Metab Eng , vol.48 , pp. 33-43
    • Young, E.M.1    Zhao, Z.2    Gielesen, B.E.M.3    Wu, L.4    Benjamin Gordon, D.5    Roubos, J.A.6    Voigt, C.A.7
  • 11
    • 84937817574 scopus 로고    scopus 로고
    • Building biological foundries for next-generation synthetic biology
    • Chao, R., Yuan, Y., Zhao, H., Building biological foundries for next-generation synthetic biology. Sci China Life Sci 58 (2015), 658–665.
    • (2015) Sci China Life Sci , vol.58 , pp. 658-665
    • Chao, R.1    Yuan, Y.2    Zhao, H.3
  • 13
    • 56649114274 scopus 로고    scopus 로고
    • A one pot, one step, precision cloning method with high throughput capability
    • Engler, C., Kandzia, R., Marillonnet, S., A one pot, one step, precision cloning method with high throughput capability. PLoS One, 3, 2008, e3647.
    • (2008) PLoS One , vol.3 , pp. e3647
    • Engler, C.1    Kandzia, R.2    Marillonnet, S.3
  • 14
    • 46949091517 scopus 로고    scopus 로고
    • Refinement and standardization of synthetic biological parts and devices
    • Canton, B., Labno, A., Endy, D., Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol, 26, 2008, 787.
    • (2008) Nat Biotechnol , vol.26 , pp. 787
    • Canton, B.1    Labno, A.2    Endy, D.3
  • 16
    • 85067179012 scopus 로고    scopus 로고
    • Ginkgo Bioworks and Zymergen scale up synthetic biology with robots
    • Bomgardner, M.M., Ginkgo Bioworks and Zymergen scale up synthetic biology with robots. Chemical & engineering news, 2016, 18–22.
    • (2016) Chemical & engineering news , pp. 18-22
    • Bomgardner, M.M.1
  • 17
    • 85036541667 scopus 로고    scopus 로고
    • Directed evolution: bringing new chemistry to life
    • Arnold, F.H., Directed evolution: bringing new chemistry to life. Angew Chem Int Ed 57 (2018), 4143–4148.
    • (2018) Angew Chem Int Ed , vol.57 , pp. 4143-4148
    • Arnold, F.H.1
  • 18
    • 85045098463 scopus 로고    scopus 로고
    • Directed evolution of protein catalysts
    • Zeymer, C., Hilvert, D., Directed evolution of protein catalysts. Annu Rev Biochem 87 (2018), 131–157.
    • (2018) Annu Rev Biochem , vol.87 , pp. 131-157
    • Zeymer, C.1    Hilvert, D.2
  • 21
    • 85013188408 scopus 로고    scopus 로고
    • Engineering of taxadiene synthase for improved selectivity and yield of a key taxol biosynthetic intermediate
    • Edgar, S., Li, F.-S., Qiao, K., Weng, J.-K., Stephanopoulos, G., Engineering of taxadiene synthase for improved selectivity and yield of a key taxol biosynthetic intermediate. ACS Synth Biol 6 (2017), 201–205.
    • (2017) ACS Synth Biol , vol.6 , pp. 201-205
    • Edgar, S.1    Li, F.-S.2    Qiao, K.3    Weng, J.-K.4    Stephanopoulos, G.5
  • 22
    • 44749083814 scopus 로고    scopus 로고
    • Metabolic engineering of taxadiene biosynthesis in yeast as a first step towards Taxol (Paclitaxel) production
    • Engels, B., Dahm, P., Jennewein, S., Metabolic engineering of taxadiene biosynthesis in yeast as a first step towards Taxol (Paclitaxel) production. Metab Eng 10 (2008), 201–206.
    • (2008) Metab Eng , vol.10 , pp. 201-206
    • Engels, B.1    Dahm, P.2    Jennewein, S.3
  • 23
    • 85045924977 scopus 로고    scopus 로고
    • Complete biosynthesis of noscapine and halogenated alkaloids in yeast
    • Yeast was engineered to produce noscapine and its analogs derived from halogenated tyrosine by expressing 25 heterologous enzymes from various organisms and 6 mutant or overexpressed endogenous yeast enzymes.
    • Engels B, Dahm P, Jennewein S: Metabolic engineering of taxadiene biosynthesis in yeast as a first step towards Taxol (Paclitaxel) production. Metabolic Engineering 2008, 10:201-206.
    • (2018) Proc Natl Acad Sci Unit States Am , vol.115 , pp. E3922
    • Li, Y.1    Li, S.2    Thodey, K.3    Trenchard, I.4    Cravens, A.5    Smolke, C.D.6
  • 24
    • 84941346066 scopus 로고    scopus 로고
    • Complete biosynthesis of opioids in yeast
    • Over 20 enzymes sourced from various organisms were expressed in yeast to reconstruct the opioid biosynthetic pathway, where enzyme mining, enzyme engineering, and optimization were employed to increase precursor supplies, improve bottlenecked steps, and facilitate cofactor recycling.
    • Galanie S, Thodey K, Trenchard IJ, Filsinger Interrante M, Smolke CD: Complete biosynthesis of opioids in yeast. Science 2015, 349:1095.
    • (2015) Science , vol.349 , pp. 1095
    • Galanie, S.1    Thodey, K.2    Trenchard, I.J.3    Filsinger Interrante, M.4    Smolke, C.D.5
  • 26
    • 84958146942 scopus 로고    scopus 로고
    • Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor
    • Zhou, H., Voigt, C.A., Vonk, B., Roubos, J.A., Bovenberg, R.A.L., Algorithmic co-optimization of genetic constructs and growth conditions: application to 6-ACA, a potential nylon-6 precursor. Nucleic Acids Res 43 (2015), 10560–10570.
    • (2015) Nucleic Acids Res , vol.43 , pp. 10560-10570
    • Zhou, H.1    Voigt, C.A.2    Vonk, B.3    Roubos, J.A.4    Bovenberg, R.A.L.5
  • 28
    • 84875265625 scopus 로고    scopus 로고
    • Metabolic engineering of muconic acid production in Saccharomyces cerevisiae
    • In vitro enzyme characterization guided the selection and construction of non-natural muconic acid pathway in yeast whose titer was further improved by genetic engineering and balanced expression of heterologous enzymes.
    • Borodina I, Kildegaard KR, Jensen NB, Blicher TH, Maury J, Sherstyk S, Schneider K, Lamosa P, Herrgard MJ, Rosenstand I, et al.: Establishing a synthetic pathway for high-level production of 3-hydroxypropionic acid in Saccharomyces cerevisiae via β-alanine. Metabolic Engineering 2015, 27:57-64.
    • (2013) Metab Eng , vol.15 , pp. 55-66
    • Curran, K.A.1    Leavitt, J.M.2    Karim, A.S.3    Alper, H.S.4
  • 29
    • 84955267195 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli for the production of cinnamaldehyde
    • Bang, H.B., Lee, Y.H., Kim, S.C., Sung, C.K., Jeong, K.J., Metabolic engineering of Escherichia coli for the production of cinnamaldehyde. Microb Cell Factories, 15, 2016, 16.
    • (2016) Microb Cell Factories , vol.15 , pp. 16
    • Bang, H.B.1    Lee, Y.H.2    Kim, S.C.3    Sung, C.K.4    Jeong, K.J.5
  • 30
    • 85057811411 scopus 로고    scopus 로고
    • Production of plant-specific flavones baicalein and scutellarein in an engineered E. coli from available phenylalanine and tyrosine
    • Li, J., Tian, C., Xia, Y., Mutanda, I., Wang, K., Wang, Y., Production of plant-specific flavones baicalein and scutellarein in an engineered E. coli from available phenylalanine and tyrosine. Metab Eng 52 (2019), 124–133.
    • (2019) Metab Eng , vol.52 , pp. 124-133
    • Li, J.1    Tian, C.2    Xia, Y.3    Mutanda, I.4    Wang, K.5    Wang, Y.6
  • 31
    • 84881223447 scopus 로고    scopus 로고
    • Biosynthesis of bioactive O-methylated flavonoids in Escherichia coli
    • Kim, M.-J., Kim, B.-G., Ahn, J.-H., Biosynthesis of bioactive O-methylated flavonoids in Escherichia coli. Appl Microbiol Biotechnol 97 (2013), 7195–7204.
    • (2013) Appl Microbiol Biotechnol , vol.97 , pp. 7195-7204
    • Kim, M.-J.1    Kim, B.-G.2    Ahn, J.-H.3
  • 32
    • 84883232076 scopus 로고    scopus 로고
    • Multivariate modular metabolic engineering of Escherichia coli to produce resveratrol from l-tyrosine
    • Wu, J., Liu, P., Fan, Y., Bao, H., Du, G., Zhou, J., Chen, J., Multivariate modular metabolic engineering of Escherichia coli to produce resveratrol from l-tyrosine. J Biotechnol 167 (2013), 404–411.
    • (2013) J Biotechnol , vol.167 , pp. 404-411
    • Wu, J.1    Liu, P.2    Fan, Y.3    Bao, H.4    Du, G.5    Zhou, J.6    Chen, J.7
  • 33
    • 84926309301 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli for the biosynthesis of various phenylpropanoid derivatives
    • Wang, S., Zhang, S., Xiao, A., Rasmussen, M., Skidmore, C., Zhan, J., Metabolic engineering of Escherichia coli for the biosynthesis of various phenylpropanoid derivatives. Metab Eng 29 (2015), 153–159.
    • (2015) Metab Eng , vol.29 , pp. 153-159
    • Wang, S.1    Zhang, S.2    Xiao, A.3    Rasmussen, M.4    Skidmore, C.5    Zhan, J.6
  • 34
    • 85042176766 scopus 로고    scopus 로고
    • An expanded plasmid-based genetic toolbox enables Cas9 genome editing and stable maintenance of synthetic pathways in phaeodactylum tricornutum
    • Slattery, S.S., Diamond, A., Wang, H., Therrien, J.A., Lant, J.T., Jazey, T., Lee, K., Klassen, Z., Desgagné-Penix, I., Karas, B.J., et al. An expanded plasmid-based genetic toolbox enables Cas9 genome editing and stable maintenance of synthetic pathways in phaeodactylum tricornutum. ACS Synth Biol 7 (2018), 328–338.
    • (2018) ACS Synth Biol , vol.7 , pp. 328-338
    • Slattery, S.S.1    Diamond, A.2    Wang, H.3    Therrien, J.A.4    Lant, J.T.5    Jazey, T.6    Lee, K.7    Klassen, Z.8    Desgagné-Penix, I.9    Karas, B.J.10
  • 36
    • 85035057487 scopus 로고    scopus 로고
    • A “plug-n-play” modular metabolic system for the production of apocarotenoids
    • Zhang, C., Chen, X., Lindley, N.D., Too, H.-P., A “plug-n-play” modular metabolic system for the production of apocarotenoids. Biotechnol Bioeng 115 (2018), 174–183.
    • (2018) Biotechnol Bioeng , vol.115 , pp. 174-183
    • Zhang, C.1    Chen, X.2    Lindley, N.D.3    Too, H.-P.4
  • 40
    • 85058527372 scopus 로고    scopus 로고
    • A combinatorial approach to study cytochrome P450 enzymes for de novo production of steviol glucosides in Baker's yeast
    • Gold, N.D., Fossati, E., Hansen, C.C., DiFalco, M., Douchin, V., Martin, V.J.J., A combinatorial approach to study cytochrome P450 enzymes for de novo production of steviol glucosides in Baker's yeast. ACS Synth Biol 7 (2018), 2918–2929.
    • (2018) ACS Synth Biol , vol.7 , pp. 2918-2929
    • Gold, N.D.1    Fossati, E.2    Hansen, C.C.3    DiFalco, M.4    Douchin, V.5    Martin, V.J.J.6
  • 41
    • 84963516758 scopus 로고    scopus 로고
    • One-step fermentative production of poly(lactate-co-glycolate) from carbohydrates in Escherichia coli
    • Choi, S.Y., Park, S.J., Kim, W.J., Yang, J.E., Lee, H., Shin, J., Lee, S.Y., One-step fermentative production of poly(lactate-co-glycolate) from carbohydrates in Escherichia coli. Nat Biotechnol, 34, 2016, 435.
    • (2016) Nat Biotechnol , vol.34 , pp. 435
    • Choi, S.Y.1    Park, S.J.2    Kim, W.J.3    Yang, J.E.4    Lee, H.5    Shin, J.6    Lee, S.Y.7
  • 42
    • 84904353331 scopus 로고    scopus 로고
    • Engineering E. coli for the biosynthesis of 3-hydroxy-γ-butyrolactone (3HBL) and 3,4-dihydroxybutyric acid (3,4-DHBA) as value-added chemicals from glucose as a sole carbon source
    • Dhamankar, H., Tarasova, Y., Martin, C.H., Prather, K.L.J., Engineering E. coli for the biosynthesis of 3-hydroxy-γ-butyrolactone (3HBL) and 3,4-dihydroxybutyric acid (3,4-DHBA) as value-added chemicals from glucose as a sole carbon source. Metab Eng 25 (2014), 72–81.
    • (2014) Metab Eng , vol.25 , pp. 72-81
    • Dhamankar, H.1    Tarasova, Y.2    Martin, C.H.3    Prather, K.L.J.4
  • 43
    • 85042799027 scopus 로고    scopus 로고
    • One-step fermentative production of aromatic polyesters from glucose by metabolically engineered Escherichia coli strains
    • Yang, J.E., Park, S.J., Kim, W.J., Kim, H.J., Kim, B.J., Lee, H., Shin, J., Lee, S.Y., One-step fermentative production of aromatic polyesters from glucose by metabolically engineered Escherichia coli strains. Nat Commun, 9, 2018, 79.
    • (2018) Nat Commun , vol.9 , pp. 79
    • Yang, J.E.1    Park, S.J.2    Kim, W.J.3    Kim, H.J.4    Kim, B.J.5    Lee, H.6    Shin, J.7    Lee, S.Y.8
  • 44
    • 79959374585 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol
    • De novo biosynthetic pathway for non-natural metabolite 1,4-butanediol was designed by an algorithm and realized experimentally in E. coli. The production was further increased by metabolic engineering guided by flux analysis.
    • Yang JE, Park SJ, Kim WJ, Kim HJ, Kim BJ, Lee H, Shin J, Lee SY: One-step fermentative production of aromatic polyesters from glucose by metabolically engineered Escherichia coli strains. Nature Communications 2018, 9:79.
    • (2011) Nat Chem Biol , vol.7 , pp. 445-452
    • Yim, H.1    Haselbeck, R.2    Niu, W.3    Pujol-Baxley, C.4    Burgard, A.5    Boldt, J.6    Khandurina, J.7    Trawick, J.D.8    Osterhout, R.E.9    Stephen, R.10
  • 45
    • 84907350970 scopus 로고    scopus 로고
    • Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path
    • A target compound is selected and the algorithm finds all paths of heterologous enzymes that lead to the pool of metabolites in a defined host. The computational design of non-native pathways to 20 commodity chemicals in E. coli is demonstrated, where 245 reaction paths are dropped into genome-scale flux models and yield is calculated under different conditions.
    • Campodonico MA, Andrews BA, Asenjo JA, Palsson BO, Feist AM: Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path. Metab Eng 2014, 25:140-158.
    • (2014) Metab Eng , vol.25 , pp. 140-158
    • Campodonico, M.A.1    Andrews, B.A.2    Asenjo, J.A.3    Palsson, B.O.4    Feist, A.M.5
  • 47
    • 84923320438 scopus 로고    scopus 로고
    • Retro-biosynthetic screening of a modular pathway design achieves selective route for microbial synthesis of 4-methyl-pentanol
    • Sheppard, M.J., Kunjapur, A.M., Wenck, S.J., Prather, K.L.J., Retro-biosynthetic screening of a modular pathway design achieves selective route for microbial synthesis of 4-methyl-pentanol. Nat Commun, 5, 2014, 5031.
    • (2014) Nat Commun , vol.5 , pp. 5031
    • Sheppard, M.J.1    Kunjapur, A.M.2    Wenck, S.J.3    Prather, K.L.J.4
  • 50
    • 29144455444 scopus 로고    scopus 로고
    • Investigation of two distinct flavone synthases for plant-specific flavone biosynthesis in Saccharomyces cerevisiae
    • Leonard, E., Yan, Y., Lim, K.H., Koffas, M.A.G., Investigation of two distinct flavone synthases for plant-specific flavone biosynthesis in Saccharomyces cerevisiae. Appl Environ Microbiol, 71, 2005, 8241.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 8241
    • Leonard, E.1    Yan, Y.2    Lim, K.H.3    Koffas, M.A.G.4
  • 51
    • 0037545559 scopus 로고    scopus 로고
    • Production of plant-specific flavanones by Escherichia coli containing an artificial gene cluster
    • Hwang, E.I., Kaneko, M., Ohnishi, Y., Horinouchi, S., Production of plant-specific flavanones by Escherichia coli containing an artificial gene cluster. Appl Environ Microbiol, 69, 2003, 2699.
    • (2003) Appl Environ Microbiol , vol.69 , pp. 2699
    • Hwang, E.I.1    Kaneko, M.2    Ohnishi, Y.3    Horinouchi, S.4
  • 53
    • 84926646130 scopus 로고    scopus 로고
    • Distributing a metabolic pathway among a microbial consortium enhances production of natural products
    • A theoretical framework is provided for comparing the benefits of putting a long pathway in one cell versus multiple cells.
    • Ajikumar PK, Xiao W-H, Tyo KEJ, Wang Y, Simeon F, Leonard E, Mucha O, Phon TH, Pfeifer B, Stephanopoulos G: Isoprenoid Pathway Optimization for Taxol Precursor Overproduction in Escherichia coli. Science 2010, 330:70.
    • (2015) Nat Biotechnol , vol.33 , pp. 377-383
    • Zhou, K.1    Qiao, K.2    Edgar, S.3    Stephanopoulos, G.4
  • 55
    • 85027022433 scopus 로고    scopus 로고
    • From waste to value – direct utilization of limonene from orange peel in a biocatalytic cascade reaction towards chiral carvolactone
    • Oberleitner, N., Ressmann, A.K., Bica, K., Gärtner, P., Fraaije, M.W., Bornscheuer, U.T., Rudroff, F., Mihovilovic, M.D., From waste to value – direct utilization of limonene from orange peel in a biocatalytic cascade reaction towards chiral carvolactone. Green Chem 19 (2017), 367–371.
    • (2017) Green Chem , vol.19 , pp. 367-371
    • Oberleitner, N.1    Ressmann, A.K.2    Bica, K.3    Gärtner, P.4    Fraaije, M.W.5    Bornscheuer, U.T.6    Rudroff, F.7    Mihovilovic, M.D.8
  • 56
    • 84974779317 scopus 로고    scopus 로고
    • Highly regio- and enantioselective multiple oxy- and amino-functionalizations of alkenes by modular cascade biocatalysis
    • 11917-11917
    • Wu, S., Zhou, Y., Wang, T., Too, H.-P., Wang, D.I.C., Li, Z., Highly regio- and enantioselective multiple oxy- and amino-functionalizations of alkenes by modular cascade biocatalysis. Nat Commun, 7, 2016 11917-11917.
    • (2016) Nat Commun , vol.7
    • Wu, S.1    Zhou, Y.2    Wang, T.3    Too, H.-P.4    Wang, D.I.C.5    Li, Z.6
  • 57
    • 84922067763 scopus 로고    scopus 로고
    • A microbial biomanufacturing platform for natural and semisynthetic opioids
    • Yeast was engineered to convert thebaine to morphine and its derivatives by expression of plant and bacterial enzymes, which was further improved by supplementation of precursor, enzyme balance, and spatial engineering.
    • Wu S, Zhou Y, Wang T, Too H-P, Wang DIC, Li Z: Highly regio- and enantioselective multiple oxy- and amino-functionalizations of alkenes by modular cascade biocatalysis. Nature Communications 2016, 7:11917-11917.
    • (2014) Nat Chem Biol , vol.10 , pp. 837
    • Thodey, K.1    Galanie, S.2    Smolke, C.D.3
  • 58
    • 0025979236 scopus 로고
    • Microbial degradation of the morphine alkaloids. Purification and characterization of morphine dehydrogenase from Pseudomonas putida M10
    • Bruce, N.C., Wilmot, C.J., Jordan, K.N., Stephens, L.D.G., Lowe, C.R., Microbial degradation of the morphine alkaloids. Purification and characterization of morphine dehydrogenase from Pseudomonas putida M10. Biochem J, 274, 1991, 875.
    • (1991) Biochem J , vol.274 , pp. 875
    • Bruce, N.C.1    Wilmot, C.J.2    Jordan, K.N.3    Stephens, L.D.G.4    Lowe, C.R.5
  • 59
    • 49949088247 scopus 로고    scopus 로고
    • Production of benzylisoquinoline alkaloids in Saccharomyces cerevisiae
    • Hawkins, K.M., Smolke, C.D., Production of benzylisoquinoline alkaloids in Saccharomyces cerevisiae. Nat Chem Biol, 4, 2008, 564.
    • (2008) Nat Chem Biol , vol.4 , pp. 564
    • Hawkins, K.M.1    Smolke, C.D.2
  • 60
    • 79960859539 scopus 로고    scopus 로고
    • Extending carbon chain length of 1-butanol pathway for 1-hexanol synthesis from glucose by engineered Escherichia coli
    • Dekishima, Y., Lan, E.I., Shen, C.R., Cho, K.M., Liao, J.C., Extending carbon chain length of 1-butanol pathway for 1-hexanol synthesis from glucose by engineered Escherichia coli. J Am Chem Soc 133 (2011), 11399–11401.
    • (2011) J Am Chem Soc , vol.133 , pp. 11399-11401
    • Dekishima, Y.1    Lan, E.I.2    Shen, C.R.3    Cho, K.M.4    Liao, J.C.5
  • 61
    • 84940460236 scopus 로고    scopus 로고
    • Production of Δ9-tetrahydrocannabinolic acid from cannabigerolic acid by whole cells of Pichia (Komagataella) pastoris expressing Δ9-tetrahydrocannabinolic acid synthase from Cannabis sativa l
    • Zirpel, B., Stehle, F., Kayser, O., Production of Δ9-tetrahydrocannabinolic acid from cannabigerolic acid by whole cells of Pichia (Komagataella) pastoris expressing Δ9-tetrahydrocannabinolic acid synthase from Cannabis sativa l. Biotechnol Lett 37 (2015), 1869–1875.
    • (2015) Biotechnol Lett , vol.37 , pp. 1869-1875
    • Zirpel, B.1    Stehle, F.2    Kayser, O.3
  • 62
    • 85023756431 scopus 로고    scopus 로고
    • Engineering yeasts as platform organisms for cannabinoid biosynthesis
    • Zirpel, B., Degenhardt, F., Martin, C., Kayser, O., Stehle, F., Engineering yeasts as platform organisms for cannabinoid biosynthesis. J Biotechnol 259 (2017), 204–212.
    • (2017) J Biotechnol , vol.259 , pp. 204-212
    • Zirpel, B.1    Degenhardt, F.2    Martin, C.3    Kayser, O.4    Stehle, F.5
  • 66
    • 84964240931 scopus 로고    scopus 로고
    • Autonomous production of 1,4-butanediol via a de novo biosynthesis pathway in engineered Escherichia coli
    • Liu, H., Lu, T., Autonomous production of 1,4-butanediol via a de novo biosynthesis pathway in engineered Escherichia coli. Metab Eng 29 (2015), 135–141.
    • (2015) Metab Eng , vol.29 , pp. 135-141
    • Liu, H.1    Lu, T.2
  • 67
    • 85012926098 scopus 로고    scopus 로고
    • Rational engineering of diol dehydratase enables 1,4-butanediol biosynthesis from xylose
    • Wang, J., Jain, R., Shen, X., Sun, X., Cheng, M., Liao, J.C., Yuan, Q., Yan, Y., Rational engineering of diol dehydratase enables 1,4-butanediol biosynthesis from xylose. Metab Eng 40 (2017), 148–156.
    • (2017) Metab Eng , vol.40 , pp. 148-156
    • Wang, J.1    Jain, R.2    Shen, X.3    Sun, X.4    Cheng, M.5    Liao, J.C.6    Yuan, Q.7    Yan, Y.8
  • 68
    • 84868098920 scopus 로고    scopus 로고
    • Controlled biosynthesis of odd-chain fuels and chemicals via engineered modular metabolic pathways
    • Tseng, H.-C., Prather, K.L.J., Controlled biosynthesis of odd-chain fuels and chemicals via engineered modular metabolic pathways. Proc Natl Acad Sci Unit States Am, 109, 2012, 17925.
    • (2012) Proc Natl Acad Sci Unit States Am , vol.109 , pp. 17925
    • Tseng, H.-C.1    Prather, K.L.J.2
  • 69
    • 84931056040 scopus 로고    scopus 로고
    • Artificial de novo biosynthesis of hydroxystyrene derivatives in a tyrosine overproducing Escherichia coli strain
    • Kang, S.-Y., Choi, O., Lee, J.K., Ahn, J.-O., Ahn, J.S., Hwang, B.Y., Hong, Y.-S., Artificial de novo biosynthesis of hydroxystyrene derivatives in a tyrosine overproducing Escherichia coli strain. Microb Cell Factories, 14, 2015, 78.
    • (2015) Microb Cell Factories , vol.14 , pp. 78
    • Kang, S.-Y.1    Choi, O.2    Lee, J.K.3    Ahn, J.-O.4    Ahn, J.S.5    Hwang, B.Y.6    Hong, Y.-S.7
  • 70
    • 84937045641 scopus 로고    scopus 로고
    • A highly selective biosynthetic pathway to non-natural C50 carotenoids assembled from moderately selective enzymes
    • Furubayashi, M., Ikezumi, M., Takaichi, S., Maoka, T., Hemmi, H., Ogawa, T., Saito, K., Tobias, A.V., Umeno, D., A highly selective biosynthetic pathway to non-natural C50 carotenoids assembled from moderately selective enzymes. Nat Commun, 6, 2015, 7534.
    • (2015) Nat Commun , vol.6 , pp. 7534
    • Furubayashi, M.1    Ikezumi, M.2    Takaichi, S.3    Maoka, T.4    Hemmi, H.5    Ogawa, T.6    Saito, K.7    Tobias, A.V.8    Umeno, D.9
  • 71
    • 84889674924 scopus 로고    scopus 로고
    • Microbial production of the aromatic building-blocks (S)-styrene oxide and (R)-1,2-phenylethanediol from renewable resources
    • McKenna, R., Pugh, S., Thompson, B., Nielsen, D.R., Microbial production of the aromatic building-blocks (S)-styrene oxide and (R)-1,2-phenylethanediol from renewable resources. Biotechnol J 8 (2013), 1465–1475.
    • (2013) Biotechnol J , vol.8 , pp. 1465-1475
    • McKenna, R.1    Pugh, S.2    Thompson, B.3    Nielsen, D.R.4
  • 73
    • 12244283725 scopus 로고    scopus 로고
    • Identification, cloning, and characterization of a Lactococcus lactis branched-chain α-keto acid decarboxylase involved in flavor formation
    • Smit, B.A., van Hylckama Vlieg, J.E.T., Engels, W.J.M., Meijer, L., Wouters, J.T.M., Smit, G., Identification, cloning, and characterization of a Lactococcus lactis branched-chain α-keto acid decarboxylase involved in flavor formation. Appl Environ Microbiol, 71, 2005, 303.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 303
    • Smit, B.A.1    van Hylckama Vlieg, J.E.T.2    Engels, W.J.M.3    Meijer, L.4    Wouters, J.T.M.5    Smit, G.6
  • 74
    • 0030885159 scopus 로고    scopus 로고
    • Purification of the Azotobacter vinelandii nifV-encoded homocitrate synthase
    • Zheng, L., White, R.H., Dean, D.R., Purification of the Azotobacter vinelandii nifV-encoded homocitrate synthase. J Bacteriol, 179, 1997, 5963.
    • (1997) J Bacteriol , vol.179 , pp. 5963
    • Zheng, L.1    White, R.H.2    Dean, D.R.3
  • 75
    • 0038236890 scopus 로고    scopus 로고
    • Purification, characterization, and molecular cloning of a novel amine:pyruvate transaminase from Vibrio fluvialis JS17
    • Shin, J.S., Yun, H., Jang, J.W., Park, I., Kim, B.G., Purification, characterization, and molecular cloning of a novel amine:pyruvate transaminase from Vibrio fluvialis JS17. Appl Microbiol Biotechnol 61 (2003), 463–471.
    • (2003) Appl Microbiol Biotechnol , vol.61 , pp. 463-471
    • Shin, J.S.1    Yun, H.2    Jang, J.W.3    Park, I.4    Kim, B.G.5
  • 76
    • 57649198304 scopus 로고    scopus 로고
    • Methanogen homoaconitase catalyzes both hydrolyase reactions in coenzyme B biosynthesis
    • Drevland, R.M., Jia, Y., Palmer, D.R.J., Graham, D.E., Methanogen homoaconitase catalyzes both hydrolyase reactions in coenzyme B biosynthesis. J Biol Chem 283 (2008), 28888–28896.
    • (2008) J Biol Chem , vol.283 , pp. 28888-28896
    • Drevland, R.M.1    Jia, Y.2    Palmer, D.R.J.3    Graham, D.E.4
  • 77
    • 84934765387 scopus 로고    scopus 로고
    • An estimate of the total DNA in the biosphere
    • Landenmark, H.K.E., Forgan, D.H., Cockell, C.S., An estimate of the total DNA in the biosphere. PLoS Biol, 13, 2015, e1002168.
    • (2015) PLoS Biol , vol.13 , pp. e1002168
    • Landenmark, H.K.E.1    Forgan, D.H.2    Cockell, C.S.3
  • 79
    • 13444280436 scopus 로고    scopus 로고
    • EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference
    • Tian, W., Arakaki, A.K., Skolnick, J., EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucleic Acids Res 32 (2004), 6226–6239.
    • (2004) Nucleic Acids Res , vol.32 , pp. 6226-6239
    • Tian, W.1    Arakaki, A.K.2    Skolnick, J.3
  • 80
    • 85035758468 scopus 로고    scopus 로고
    • Enzyme evolution: innovation is easy, optimization is complicated
    • Newton, M.S., Arcus, V.L., Gerth, M.L., Patrick, W.M., Enzyme evolution: innovation is easy, optimization is complicated. Curr Opin Struct Biol 48 (2018), 110–116.
    • (2018) Curr Opin Struct Biol , vol.48 , pp. 110-116
    • Newton, M.S.1    Arcus, V.L.2    Gerth, M.L.3    Patrick, W.M.4
  • 82
    • 85067173349 scopus 로고    scopus 로고
    • NCBI reference sequence (RefSeq) database distribution release notes
    • This estimate is based on the 135,670,032 proteins in the NCBI database in 2019 and the estimation that 30% are enzymes from Tian et al. EFICAz: a comprehensive approach for accurate genome-scale enzyme function inference. Nucleic Acids Research 2004, 32:6226–6239.
    • Lipman DJ, Benson DA, Karsch-Mizrachi I, Ostell J, Clark K, Cavanaugh M, Sayers EW: GenBank. Nucleic Acids Research 2016, 45:D37-D42.
    • (2019) Release , vol.93
  • 84
    • 79959931985 scopus 로고    scopus 로고
    • HMMER web server: interactive sequence similarity searching
    • Finn, R.D., Clements, J., Eddy, S.R., HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 39 (2011), W29–W37.
    • (2011) Nucleic Acids Res , vol.39 , pp. W29-W37
    • Finn, R.D.1    Clements, J.2    Eddy, S.R.3
  • 86
    • 38049001166 scopus 로고    scopus 로고
    • Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
    • Atsumi, S., Hanai, T., Liao, J.C., Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451 (2008), 86–89.
    • (2008) Nature , vol.451 , pp. 86-89
    • Atsumi, S.1    Hanai, T.2    Liao, J.C.3
  • 88
    • 79955611425 scopus 로고    scopus 로고
    • Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli
    • Shen, C.R., Lan, E.I., Dekishima, Y., Baez, A., Cho, K.M., Liao, J.C., Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli. Appl Environ Microbiol 77 (2011), 2905–2915.
    • (2011) Appl Environ Microbiol , vol.77 , pp. 2905-2915
    • Shen, C.R.1    Lan, E.I.2    Dekishima, Y.3    Baez, A.4    Cho, K.M.5    Liao, J.C.6
  • 89
    • 84906043265 scopus 로고    scopus 로고
    • Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry
    • Heins, R.A., Cheng, X., Nath, S., Deng, K., Bowen, B.P., Chivian, D.C., Datta, S., Friedland, G.D., D'Haeseleer, P., Wu, D., et al. Phylogenomically guided identification of industrially relevant GH1 β-glucosidases through DNA synthesis and nanostructure-initiator mass spectrometry. ACS Chem Biol 9 (2014), 2082–2091.
    • (2014) ACS Chem Biol , vol.9 , pp. 2082-2091
    • Heins, R.A.1    Cheng, X.2    Nath, S.3    Deng, K.4    Bowen, B.P.5    Chivian, D.C.6    Datta, S.7    Friedland, G.D.8    D'Haeseleer, P.9    Wu, D.10
  • 91
    • 84907822164 scopus 로고    scopus 로고
    • Biosynthesis of taxadiene in Saccharomyces cerevisiae: selection of geranylgeranyl diphosphate synthase directed by a computer-aided docking strategy
    • e109348-e109348
    • Ding, M.z., Yan, H.f., Li, L-f, Zhai, F., Shang, L-q, Yin, Z., Yuan, Y-j, Biosynthesis of taxadiene in Saccharomyces cerevisiae: selection of geranylgeranyl diphosphate synthase directed by a computer-aided docking strategy. PLoS One, 9, 2014 e109348-e109348.
    • (2014) PLoS One , vol.9
    • Ding, M.Z.1    Yan, H.F.2    Li, L.-F.3    Zhai, F.4    Shang, L.-Q.5    Yin, Z.6    Yuan, Y.-J.7
  • 92
    • 84930804841 scopus 로고    scopus 로고
    • Highly active and specific tyrosine ammonia-lyases from diverse origins enable enhanced production of aromatic compounds in bacteria and Saccharomyces cerevisiae
    • Jendresen, C.B., Stahlhut, S.G., Li, M., Gaspar, P., Siedler, S., Förster, J., Maury, J., Borodina, I., Nielsen, A.T., Highly active and specific tyrosine ammonia-lyases from diverse origins enable enhanced production of aromatic compounds in bacteria and Saccharomyces cerevisiae. Appl Environ Microbiol 81 (2015), 4458–4476.
    • (2015) Appl Environ Microbiol , vol.81 , pp. 4458-4476
    • Jendresen, C.B.1    Stahlhut, S.G.2    Li, M.3    Gaspar, P.4    Siedler, S.5    Förster, J.6    Maury, J.7    Borodina, I.8    Nielsen, A.T.9
  • 93
    • 85009935517 scopus 로고    scopus 로고
    • Metabolic engineering of Saccharomyces cerevisiae for de novo production of dihydrochalcones with known antioxidant, antidiabetic, and sweet tasting properties
    • Eichenberger, M., Lehka, B.J., Folly, C., Fischer, D., Martens, S., Simón, E., Naesby, M., Metabolic engineering of Saccharomyces cerevisiae for de novo production of dihydrochalcones with known antioxidant, antidiabetic, and sweet tasting properties. Metab Eng 39 (2017), 80–89.
    • (2017) Metab Eng , vol.39 , pp. 80-89
    • Eichenberger, M.1    Lehka, B.J.2    Folly, C.3    Fischer, D.4    Martens, S.5    Simón, E.6    Naesby, M.7
  • 95
    • 85057169042 scopus 로고    scopus 로고
    • β-Glucosidase discovery and design for the degradation of oleuropein
    • Guggenheim, K.G., Crawford, L.M., Paradisi, F., Wang, S.C., Siegel, J.B., β-Glucosidase discovery and design for the degradation of oleuropein. ACS Omega 3 (2018), 15754–15762.
    • (2018) ACS Omega , vol.3 , pp. 15754-15762
    • Guggenheim, K.G.1    Crawford, L.M.2    Paradisi, F.3    Wang, S.C.4    Siegel, J.B.5
  • 98
    • 84875317202 scopus 로고    scopus 로고
    • A systematic comparison of the MetaCyc and KEGG pathway databases
    • Altman, T., Travers, M., Kothari, A., Caspi, R., Karp, P.D., A systematic comparison of the MetaCyc and KEGG pathway databases. BMC Bioinf, 14, 2013, 112.
    • (2013) BMC Bioinf , vol.14 , pp. 112
    • Altman, T.1    Travers, M.2    Kothari, A.3    Caspi, R.4    Karp, P.D.5
  • 102
    • 85020822860 scopus 로고    scopus 로고
    • antiSMASH 4.0—improvements in chemistry prediction and gene cluster boundary identification
    • AntiSMASH analyzes proteins encoded in the DNA sequence using profile Hidden Markov Models and makes bacterial / fungal biosynthetic gene cluster prediction based on a set of man-curated rules.
    • Blin K, Weber T, Lee SY, Medema MH, Pascal Andreu V, de los Santos EL C, Del Carratore F: The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters. Nucleic Acids Research 2018, 47:D625-D630.
    • (2017) Nucleic Acids Res , vol.45 , pp. W36-W41
    • Blin, K.1    Wolf, T.2    Chevrette, M.G.3    Lu, X.4    Schwalen, C.J.5    Kautsar, S.A.6    Suarez Duran, H.G.7    de los Santos Emmanuel, L.C.8    Kim, H.U.9    Nave, M.10
  • 104
    • 84948178435 scopus 로고    scopus 로고
    • Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway
    • In searching for ketoisovalerate decarboxylase homologs that prefer C8 substrates ligand-enzyme models using Rosetta Design effectively prioritized 10 out of 239 candidates.
    • Gerlt JA, Bouvier JT, Davidson DB, Imker HJ, Sadkhin B, Slater DR, Whalen KL: Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST): A web tool for generating protein sequence similarity networks. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 2015, 1854:1019-1037.
    • (2015) Nat Commun , vol.6 , pp. 1-9
    • Mak, W.S.1    Tran, S.2    Marcheschi, R.3    Bertolani, S.4    Thompson, J.5    Baker, D.6    Liao, J.C.7    Siegel, J.B.8
  • 105
    • 85042930684 scopus 로고    scopus 로고
    • Exploration of enzyme diversity by integrating bioinformatics with expression analysis and biochemical characterization
    • An enzyme mining effort where homology models guided the calculation of ligand binding pocket volume. This was used to narrow down 658 dehalogenases to a set of 20 that are screened for their substrate profile using robotic automation.
    • Vanacek P, Sebestova E, Babkova P, Bidmanova S, Daniel L, Dvorak P, Stepankova V, Chaloupkova R, Brezovsky J, Prokop Z, et al.: Exploration of enzyme diversity by integrating bioinformatics with expression analysis and biochemical characterization. ACS Catal 2018, 8:2402-2412.
    • (2018) ACS Catal , vol.8 , pp. 2402-2412
    • Vanacek, P.1    Sebestova, E.2    Babkova, P.3    Bidmanova, S.4    Daniel, L.5    Dvorak, P.6    Stepankova, V.7    Chaloupkova, R.8    Brezovsky, J.9    Prokop, Z.10
  • 107
    • 84899696363 scopus 로고    scopus 로고
    • Large-scale de novo DNA synthesis: technologies and applications
    • Kosuri, S., Church, G.M., Large-scale de novo DNA synthesis: technologies and applications. Nat Methods 11 (2014), 499–507.
    • (2014) Nat Methods , vol.11 , pp. 499-507
    • Kosuri, S.1    Church, G.M.2
  • 108
    • 84958130483 scopus 로고    scopus 로고
    • Time for new DNA synthesis and sequencing cost curves
    • Carlson, R., Time for new DNA synthesis and sequencing cost curves. 2014 https://synbiobeta.com/time-new-dna-synthesis-sequencing-cost-curves-rob-carlson/.
    • (2014)
    • Carlson, R.1
  • 109
    • 85015318933 scopus 로고    scopus 로고
    • Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase
    • An ultrahigh-throughput droplet-based microfluidic screening was applied to improve the activity of a computationally designed aldolase.
    • Carlson R: Time for New DNA Synthesis and Sequencing Cost Curves. 2014:https://synbiobeta.com/time-new-dna-synthesis-sequencing-cost-curves-rob-carlson/.
    • (2016) Nat Chem , vol.9 , pp. 50
    • Obexer, R.1    Godina, A.2    Garrabou, X.3    Mittl, P.R.E.4    Baker, D.5    Griffiths, A.D.6    Hilvert, D.7
  • 112
    • 17444433274 scopus 로고    scopus 로고
    • Exploration of natural and artificial sequence spaces: towards a functional remodeling of membrane-bound cytochrome P450
    • Abécassis, V., Urban, P., Aggerbeck, L., Truan, G., Pompon, D., Exploration of natural and artificial sequence spaces: towards a functional remodeling of membrane-bound cytochrome P450. Biocatal Biotransform 21 (2003), 55–66.
    • (2003) Biocatal Biotransform , vol.21 , pp. 55-66
    • Abécassis, V.1    Urban, P.2    Aggerbeck, L.3    Truan, G.4    Pompon, D.5
  • 113
    • 85016932092 scopus 로고    scopus 로고
    • Exploring sequence space in search of functional enzymes using microfluidic droplets
    • Mair, P., Gielen, F., Hollfelder, F., Exploring sequence space in search of functional enzymes using microfluidic droplets. Curr Opin Chem Biol 37 (2017), 137–144.
    • (2017) Curr Opin Chem Biol , vol.37 , pp. 137-144
    • Mair, P.1    Gielen, F.2    Hollfelder, F.3
  • 114
    • 85044208149 scopus 로고    scopus 로고
    • Efficient molecular evolution to generate enantioselective enzymes using a dual-channel microfluidic droplet screening platform
    • Ma, F., Chung, M.T., Yao, Y., Nidetz, R., Lee, L.M., Liu, A.P., Feng, Y., Kurabayashi, K., Yang, G.-Y., Efficient molecular evolution to generate enantioselective enzymes using a dual-channel microfluidic droplet screening platform. Nat Commun, 9, 2018, 1030.
    • (2018) Nat Commun , vol.9 , pp. 1030
    • Ma, F.1    Chung, M.T.2    Yao, Y.3    Nidetz, R.4    Lee, L.M.5    Liu, A.P.6    Feng, Y.7    Kurabayashi, K.8    Yang, G.-Y.9
  • 115
    • 85041385092 scopus 로고    scopus 로고
    • Speeding up enzyme discovery and engineering with ultrahigh-throughput methods
    • Bunzel, H.A., Garrabou, X., Pott, M., Hilvert, D., Speeding up enzyme discovery and engineering with ultrahigh-throughput methods. Curr Opin Struct Biol 48 (2018), 149–156.
    • (2018) Curr Opin Struct Biol , vol.48 , pp. 149-156
    • Bunzel, H.A.1    Garrabou, X.2    Pott, M.3    Hilvert, D.4
  • 116
    • 84996478400 scopus 로고    scopus 로고
    • Ultrahigh-throughput–directed enzyme evolution by absorbance-activated droplet sorting (AADS)
    • + dependent dye assay enables the assaying of >1,000,000 mutants per hour using a sorter.
    • Bunzel HA, Garrabou X, Pott M, Hilvert D: Speeding up enzyme discovery and engineering with ultrahigh-throughput methods. Current Opinion in Structural Biology 2018, 48:149-156.
    • (2016) Proc Natl Acad Sci Unit States Am , vol.113 , pp. E7383-E7389
    • Gielen, F.1    Hours, R.2    Emond, S.3    Fischlechner, M.4    Schell, U.5    Hollfelder, F.6
  • 117
    • 2242424513 scopus 로고    scopus 로고
    • Enzyme fingerprints of activity, and stereo- and enantioselectivity from fluorogenic and chromogenic substrate arrays
    • Wahler, D., Badalassi, F., Crotti, P., Reymond, J.-L., Enzyme fingerprints of activity, and stereo- and enantioselectivity from fluorogenic and chromogenic substrate arrays. Chem Eur J 8 (2002), 3211–3228.
    • (2002) Chem Eur J , vol.8 , pp. 3211-3228
    • Wahler, D.1    Badalassi, F.2    Crotti, P.3    Reymond, J.-L.4
  • 118
    • 3543062056 scopus 로고    scopus 로고
    • Classifying enzymes from selectivity fingerprints
    • Grognux, J., Reymond, J.-L., Classifying enzymes from selectivity fingerprints. Chembiochem 5 (2004), 826–831.
    • (2004) Chembiochem , vol.5 , pp. 826-831
    • Grognux, J.1    Reymond, J.-L.2
  • 119
    • 0038601676 scopus 로고    scopus 로고
    • Enzymatic profiling system in a small-molecule microarray
    • Zhu, Q., Uttamchandani, M., Li, D., Lesaicherre, M.L., Yao, S.Q., Enzymatic profiling system in a small-molecule microarray. Org Lett 5 (2003), 1257–1260.
    • (2003) Org Lett , vol.5 , pp. 1257-1260
    • Zhu, Q.1    Uttamchandani, M.2    Li, D.3    Lesaicherre, M.L.4    Yao, S.Q.5
  • 120
    • 85004191344 scopus 로고    scopus 로고
    • Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli
    • Metabolome extract of E. coli was treated with cell lysate from E. coli expressing the target enzyme or its purified form. Non-targeted mass spectrometry was used to detect the change in metabolomes and assign function to 214 out of 1275 uncharacaterized E. coli enzymes.
    • Zhu Q, Uttamchandani M, Li D, Lesaicherre ML, Yao SQ: Enzymatic Profiling System in a Small-Molecule Microarray. Organic Letters 2003, 5:1257-1260.
    • (2016) Nat Methods , vol.14 , pp. 187
    • Sévin, D.C.1    Fuhrer, T.2    Zamboni, N.3    Sauer, U.4
  • 121
    • 85045003056 scopus 로고    scopus 로고
    • Enzymatic construction of highly strained carbocycles
    • Chen, K., Huang, X., Kan, S.B.J., Zhang, R.K., Arnold, F.H., Enzymatic construction of highly strained carbocycles. Science 360 (2018), 71–75.
    • (2018) Science , vol.360 , pp. 71-75
    • Chen, K.1    Huang, X.2    Kan, S.B.J.3    Zhang, R.K.4    Arnold, F.H.5
  • 122
    • 84997080010 scopus 로고    scopus 로고
    • Directed evolution of cytochrome c for carbon-silicon bond formation: bringing silicon to life
    • Cytochrome c from Rhodothermus marinus was enigeered to catalyze highly selective carbene insertion into silicon–hydrogen bond on various organosilicon compounds both in vivo and in vitro.
    • Chen K, Huang X, Kan SBJ, Zhang RK, Arnold FH: Enzymatic construction of highly strained carbocycles. Science 2018, 360:71-75.
    • (2016) Science , vol.354 , pp. 1048-1051
    • Kan, S.B.J.1    Lewis, R.D.2    Chen, K.3    Arnold, F.H.4
  • 123
    • 85034447569 scopus 로고    scopus 로고
    • Shining a light on enzyme promiscuity
    • Copley, S.D., Shining a light on enzyme promiscuity. Curr Opin Struct Biol 47 (2017), 167–175.
    • (2017) Curr Opin Struct Biol , vol.47 , pp. 167-175
    • Copley, S.D.1
  • 124
    • 77953623874 scopus 로고    scopus 로고
    • Enzyme promiscuity: a mechanistic and evolutionary perspective
    • Tawfik, OKaDS., Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu Rev Biochem 79 (2010), 471–505.
    • (2010) Annu Rev Biochem , vol.79 , pp. 471-505
    • Tawfik, O.K.S.1
  • 125
    • 84955395472 scopus 로고    scopus 로고
    • Enzyme engineering by directed evolution
    • K. Drauz H. Waldmann Wiley-VCH
    • May, O., Voigt, C.A., Arnold, F.H., Enzyme engineering by directed evolution. Drauz, K., Waldmann, H., (eds.) Enzyme catalysis in organic synthesis, 2002, Wiley-VCH, 95–138.
    • (2002) Enzyme catalysis in organic synthesis , pp. 95-138
    • May, O.1    Voigt, C.A.2    Arnold, F.H.3
  • 126
    • 84928253931 scopus 로고    scopus 로고
    • Panoramic view of a superfamily of phosphatases through substrate profiling
    • Representative 217 phosphatases from diverse prokaryote species were expressed and their activity against a set of 167 substrates tested. The results revealed the different substrate specificity among these enzymes, which could be used to infer enzyme functions for unchacaterized phosphates.
    • May O, Voigt CA, Arnold FH: Enzyme Engineering by Directed Evolution. In Enzyme Catalysis in Organic Synthesis. Edited by Drauz K, Waldmann H. Wiley-VCH; 2002:95-138.
    • (2015) Proc Natl Acad Sci Unit States Am , vol.112 , pp. E1974-E1983
    • Huang, H.1    Pandya, C.2    Liu, C.3    Al-Obaidi, N.F.4    Wang, M.5    Zheng, L.6    Toews Keating, S.7    Aono, M.8    Love, J.D.9    Evans, B.10
  • 127
    • 53549085133 scopus 로고    scopus 로고
    • Evolutionary history of a specialized P450 propane monooxygenase
    • Fasan, R., Meharenna, Y.T., Snow, C.D., Poulos, T.L., Arnold, F.H., Evolutionary history of a specialized P450 propane monooxygenase. J Mol Biol 383 (2008), 1069–1080.
    • (2008) J Mol Biol , vol.383 , pp. 1069-1080
    • Fasan, R.1    Meharenna, Y.T.2    Snow, C.D.3    Poulos, T.L.4    Arnold, F.H.5
  • 128
    • 85050490816 scopus 로고    scopus 로고
    • Complete switch of reaction specificity of an aldolase by directed evolution in vitro: synthesis of generic aliphatic aldol products
    • Junker, S., Roldan, R., Joosten, H.-J., Clapés, P., Fessner, W.-D., Complete switch of reaction specificity of an aldolase by directed evolution in vitro: synthesis of generic aliphatic aldol products. Angew Chem Int Ed 57 (2018), 10153–10157.
    • (2018) Angew Chem Int Ed , vol.57 , pp. 10153-10157
    • Junker, S.1    Roldan, R.2    Joosten, H.-J.3    Clapés, P.4    Fessner, W.-D.5
  • 130
    • 84922359242 scopus 로고    scopus 로고
    • Differential effects of a mutation on the normal and promiscuous activities of orthologs: implications for natural and directed evolution
    • Khanal, A., Kershner, J.P., Yu McLoughlin, S., Copley, S.D., Differential effects of a mutation on the normal and promiscuous activities of orthologs: implications for natural and directed evolution. Mol Biol Evol 32 (2014), 100–108.
    • (2014) Mol Biol Evol , vol.32 , pp. 100-108
    • Khanal, A.1    Kershner, J.P.2    Yu McLoughlin, S.3    Copley, S.D.4
  • 131
    • 84977074385 scopus 로고    scopus 로고
    • Mutations closer to the active site improve the promiscuous aldolase activity of 4-oxalocrotonate tautomerase more effectively than distant mutations
    • Rahimi, M., van der Meer, J.-Y., Geertsema, E.M., Poddar, H., Baas, B.-J., Poelarends, G.J., Mutations closer to the active site improve the promiscuous aldolase activity of 4-oxalocrotonate tautomerase more effectively than distant mutations. Chembiochem 17 (2016), 1225–1228.
    • (2016) Chembiochem , vol.17 , pp. 1225-1228
    • Rahimi, M.1    van der Meer, J.-Y.2    Geertsema, E.M.3    Poddar, H.4    Baas, B.-J.5    Poelarends, G.J.6
  • 133
    • 28444439905 scopus 로고    scopus 로고
    • How to broaden enzyme substrate specificity: strategies, implications and applications
    • Jestin, J.-L., Vichier-Guerre, S., How to broaden enzyme substrate specificity: strategies, implications and applications. Res Microbiol 156 (2005), 961–966.
    • (2005) Res Microbiol , vol.156 , pp. 961-966
    • Jestin, J.-L.1    Vichier-Guerre, S.2
  • 134
    • 84976584288 scopus 로고    scopus 로고
    • Broadening substrate specificity of a chain-extending ketosynthase through a single active-site mutation
    • Murphy, A.C., Hong, H., Vance, S., Broadhurst, R.W., Leadlay, P.F., Broadening substrate specificity of a chain-extending ketosynthase through a single active-site mutation. Chem Commun 52 (2016), 8373–8376.
    • (2016) Chem Commun , vol.52 , pp. 8373-8376
    • Murphy, A.C.1    Hong, H.2    Vance, S.3    Broadhurst, R.W.4    Leadlay, P.F.5
  • 135
    • 85026743386 scopus 로고    scopus 로고
    • Recent advances in enzyme promiscuity
    • Gupta, R.D., Recent advances in enzyme promiscuity. Sustain Chem Proc, 4, 2016, 2.
    • (2016) Sustain Chem Proc , vol.4 , pp. 2
    • Gupta, R.D.1
  • 136
    • 10044248344 scopus 로고    scopus 로고
    • Catalytic promiscuity in biocatalysis: using old enzymes to form new bonds and follow new pathways
    • Bornscheuer, U.T., Kazlauskas, R.J., Catalytic promiscuity in biocatalysis: using old enzymes to form new bonds and follow new pathways. Angew Chem Int Ed 43 (2004), 6032–6040.
    • (2004) Angew Chem Int Ed , vol.43 , pp. 6032-6040
    • Bornscheuer, U.T.1    Kazlauskas, R.J.2
  • 140
    • 33748802003 scopus 로고    scopus 로고
    • Structural basis for ligand promiscuity in cytochrome P450 3A4
    • Ekroos, M., Sjögren, T., Structural basis for ligand promiscuity in cytochrome P450 3A4. Proc Natl Acad Sci Unit States Am 103 (2006), 13682–13687.
    • (2006) Proc Natl Acad Sci Unit States Am , vol.103 , pp. 13682-13687
    • Ekroos, M.1    Sjögren, T.2
  • 141
    • 85013252693 scopus 로고    scopus 로고
    • Modeling reactivity to biological macromolecules with a deep multitask network
    • Hughes, T.B., Dang, N.L., Miller, G.P., Swamidass, S.J., Modeling reactivity to biological macromolecules with a deep multitask network. ACS Cent Sci 2 (2016), 529–537.
    • (2016) ACS Cent Sci , vol.2 , pp. 529-537
    • Hughes, T.B.1    Dang, N.L.2    Miller, G.P.3    Swamidass, S.J.4
  • 142
    • 84896506204 scopus 로고    scopus 로고
    • XenoSite: accurately predicting CYP-mediated sites of metabolism with neural networks
    • Zaretzki, J., Matlock, M., Swamidass, S.J., XenoSite: accurately predicting CYP-mediated sites of metabolism with neural networks. J Chem Inf Model 53 (2013), 3373–3383.
    • (2013) J Chem Inf Model , vol.53 , pp. 3373-3383
    • Zaretzki, J.1    Matlock, M.2    Swamidass, S.J.3
  • 143
    • 85047102931 scopus 로고    scopus 로고
    • CypReact: a software tool for in silico reactant prediction for human cytochrome P450 enzymes
    • Tian, S., Djoumbou-Feunang, Y., Greiner, R., Wishart, D.S., CypReact: a software tool for in silico reactant prediction for human cytochrome P450 enzymes. J Chem Inf Model 58 (2018), 1282–1291.
    • (2018) J Chem Inf Model , vol.58 , pp. 1282-1291
    • Tian, S.1    Djoumbou-Feunang, Y.2    Greiner, R.3    Wishart, D.S.4
  • 146
    • 84931574824 scopus 로고    scopus 로고
    • Methods for the directed evolution of proteins
    • Packer, M.S., Liu, D.R., Methods for the directed evolution of proteins. Nat Rev Genet 16 (2015), 379–394.
    • (2015) Nat Rev Genet , vol.16 , pp. 379-394
    • Packer, M.S.1    Liu, D.R.2
  • 147
    • 84921037626 scopus 로고    scopus 로고
    • Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently
    • Currin, A., Swainston, N., Day, P.J., Kell, D.B., Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently. Chem Soc Rev 44 (2015), 1172–1239.
    • (2015) Chem Soc Rev , vol.44 , pp. 1172-1239
    • Currin, A.1    Swainston, N.2    Day, P.J.3    Kell, D.B.4
  • 148
    • 84920913613 scopus 로고    scopus 로고
    • Improving and repurposing biocatalysts via directed evolution
    • Denard, C.A., Ren, H., Zhao, H., Improving and repurposing biocatalysts via directed evolution. Curr Opin Chem Biol 25 (2015), 55–64.
    • (2015) Curr Opin Chem Biol , vol.25 , pp. 55-64
    • Denard, C.A.1    Ren, H.2    Zhao, H.3
  • 150
    • 84872495336 scopus 로고    scopus 로고
    • Olefin cyclopropanation via carbene transfer catalyzed by engineered cytochrome P450 enzymes
    • BM3 was engineered to catalyze diastereo- and stereoselective cycloproponation on variou.
    • Hammer SC, Knight AM, Arnold FH: Design and evolution of enzymes for non-natural chemistry. Current Opinion in Green and Sustainable Chemistry 2017, 7:23-30.
    • (2013) Science , vol.339 , pp. 307-310
    • Coelho, P.S.1    Brustad, E.M.2    Kannan, A.3    Arnold, F.H.4
  • 151
    • 85040338163 scopus 로고    scopus 로고
    • Genetically programmed chiral organoborane synthesis
    • Cytochrome c from Rhodothermus marinus was enigeered to catalyze highly selective carbene insertion into boron–hydrogen bond on various N-heterocyclic carbene borane compounds both in vivo and in vitro.
    • Jennifer Kan SB, Huang X, Gumulya Y, Chen K, Arnold FH: Genetically programmed chiral organoborane synthesis. Nature 2017, 552:132-136.
    • (2017) Nature , vol.552 , pp. 132-136
    • Jennifer Kan, S.B.1    Huang, X.2    Gumulya, Y.3    Chen, K.4    Arnold, F.H.5
  • 155
    • 84899824651 scopus 로고    scopus 로고
    • De novo computational enzyme design
    • Zanghellini, A., De novo computational enzyme design. Curr Opin Biotechnol 29 (2014), 132–138.
    • (2014) Curr Opin Biotechnol , vol.29 , pp. 132-138
    • Zanghellini, A.1
  • 156
    • 78649857195 scopus 로고    scopus 로고
    • Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5′-phosphate synthesis
    • Kim, J., Kershner, J.P., Novikov, Y., Shoemaker, R.K., Copley, S.D., Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5′-phosphate synthesis. Mol Syst Biol, 6, 2010, 436.
    • (2010) Mol Syst Biol , vol.6 , pp. 436
    • Kim, J.1    Kershner, J.P.2    Novikov, Y.3    Shoemaker, R.K.4    Copley, S.D.5
  • 157
    • 77955353890 scopus 로고    scopus 로고
    • Molecular signatures-based prediction of enzyme promiscuity
    • Faulon, J.-L., Carbonell, P., Molecular signatures-based prediction of enzyme promiscuity. Bioinformatics 26 (2010), 2012–2019.
    • (2010) Bioinformatics , vol.26 , pp. 2012-2019
    • Faulon, J.-L.1    Carbonell, P.2
  • 158
    • 0000183514 scopus 로고
    • Computer-assisted synthetic analysis. Facile man-machine communication of chemical structure by interactive computer graphics
    • Corey, E.J., Wipke, W.T., Cramer, R.D., Howe, W.J., Computer-assisted synthetic analysis. Facile man-machine communication of chemical structure by interactive computer graphics. J Am Chem Soc 94 (1972), 421–430.
    • (1972) J Am Chem Soc , vol.94 , pp. 421-430
    • Corey, E.J.1    Wipke, W.T.2    Cramer, R.D.3    Howe, W.J.4
  • 159
    • 37049231053 scopus 로고
    • Computer-Assisted design of complex organic syntheses
    • Corey, E.J., Wipke, W.T., Computer-Assisted design of complex organic syntheses. Science 166 (1969), 178–192.
    • (1969) Science , vol.166 , pp. 178-192
    • Corey, E.J.1    Wipke, W.T.2
  • 161
    • 85044660186 scopus 로고    scopus 로고
    • Planning chemical syntheses with deep neural networks and symbolic AI
    • Based on rules extracted from Reaxys, a retrosynthesis algorithm uses three neural networks that predict the best reactions to make a product, limit reactions to those that are feasible, and estimate the position value. The tree is searched using a Monte Carlo algorithm.
    • Segler MHS, Preuss M, Waller MP: Planning chemical syntheses with deep neural networks and symbolic AI. Nature 2018, 555:604-610.
    • (2018) Nature , vol.555 , pp. 604-610
    • Segler, M.H.S.1    Preuss, M.2    Waller, M.P.3
  • 162
    • 85050536432 scopus 로고    scopus 로고
    • “Found in Translation”: predicting outcomes of complex organic chemistry reactions using neural sequence-to-sequence models
    • Schwaller, P., Gaudin, T., Lányi, D., Bekas, C., Laino, T., “Found in Translation”: predicting outcomes of complex organic chemistry reactions using neural sequence-to-sequence models. Chem Sci 9 (2018), 6091–6098.
    • (2018) Chem Sci , vol.9 , pp. 6091-6098
    • Schwaller, P.1    Gaudin, T.2    Lányi, D.3    Bekas, C.4    Laino, T.5
  • 163
    • 85039042492 scopus 로고    scopus 로고
    • Artificial intelligence in synthetic chemistry: achievements and prospects
    • Baskin II, Madzhidov, T.I., Antipin, I.S., Varnek, A.A., Artificial intelligence in synthetic chemistry: achievements and prospects. Russian Chem Rev 86 (2017), 1127–1156.
    • (2017) Russian Chem Rev , vol.86 , pp. 1127-1156
    • Baskin1    Madzhidov, T.I.2    Antipin, I.S.3    Varnek, A.A.4
  • 167
    • 84867780136 scopus 로고    scopus 로고
    • Reaction Predictor: prediction of complex chemical reactions at the mechanistic level using machine learning
    • Kayala, M.A., Baldi, P., Reaction Predictor: prediction of complex chemical reactions at the mechanistic level using machine learning. J Chem Inf Model 52 (2012), 2526–2540.
    • (2012) J Chem Inf Model , vol.52 , pp. 2526-2540
    • Kayala, M.A.1    Baldi, P.2
  • 168
    • 85047214574 scopus 로고    scopus 로고
    • Machine learning in computer-aided synthesis planning
    • Coley, C.W., Green, W.H., Jensen, K.F., Machine learning in computer-aided synthesis planning. Acc Chem Res 51 (2018), 1281–1289.
    • (2018) Acc Chem Res , vol.51 , pp. 1281-1289
    • Coley, C.W.1    Green, W.H.2    Jensen, K.F.3
  • 169
    • 85055039018 scopus 로고    scopus 로고
    • Artificial intelligence: the future for organic chemistry?
    • Peiretti, F., Brunel, J.M., Artificial intelligence: the future for organic chemistry?. ACS Omega 3 (2018), 13263–13266.
    • (2018) ACS Omega , vol.3 , pp. 13263-13266
    • Peiretti, F.1    Brunel, J.M.2
  • 170
    • 67649791997 scopus 로고    scopus 로고
    • Machine learning of chemical reactivity from databases of organic reactions
    • Carrera, G.V.S.M., Gupta, S., Aires-de-Sousa, J., Machine learning of chemical reactivity from databases of organic reactions. J Comput Aided Mol Des 23 (2009), 419–429.
    • (2009) J Comput Aided Mol Des , vol.23 , pp. 419-429
    • Carrera, G.V.S.M.1    Gupta, S.2    Aires-de-Sousa, J.3
  • 172
    • 33747874402 scopus 로고    scopus 로고
    • The core and most useful molecules in organic chemistry
    • Bishop, K.J.M., Klajn, R., Grzybowski, B.A., The core and most useful molecules in organic chemistry. Angew Chem Int Ed 45 (2006), 5348–5354.
    • (2006) Angew Chem Int Ed , vol.45 , pp. 5348-5354
    • Bishop, K.J.M.1    Klajn, R.2    Grzybowski, B.A.3
  • 173
    • 85067187563 scopus 로고    scopus 로고
    • Reaxys.
    • Reaxys. https://www.reaxys.com/.
  • 174
    • 85041906939 scopus 로고    scopus 로고
    • Statistics of the network of organic chemistry
    • Jacob, P.-M., Lapkin, A., Statistics of the network of organic chemistry. React Chem Eng 3 (2018), 102–118.
    • (2018) React Chem Eng , vol.3 , pp. 102-118
    • Jacob, P.-M.1    Lapkin, A.2
  • 175
    • 85050349135 scopus 로고    scopus 로고
    • Computational chemical synthesis analysis and pathway design
    • 199-199
    • Feng, F., Lai, L., Pei, J., Computational chemical synthesis analysis and pathway design. Front Chem, 6, 2018 199-199.
    • (2018) Front Chem , vol.6
    • Feng, F.1    Lai, L.2    Pei, J.3
  • 177
    • 67949084937 scopus 로고    scopus 로고
    • The 'wired' universe of organic chemistry
    • The Network of Organic Chemistry is searched to identify chemicals of broad utility and to identify “islands” to which there is no synthetic route (typically natural products).
    • Kowalik M, Gothard CM, Drews AM, Gothard NA, Weckiewicz A, Fuller PE, Grzybowski BA, Bishop KJM: Parallel optimization of synthetic pathways within the network of organic chemistry. Angewandte Chemie - International Edition 2012, 51:7928-7932.
    • (2009) Nat Chem , vol.1 , pp. 31-36
    • Grzybowski, B.A.1    Bishop, K.J.M.2    Kowalczyk, B.3    Wilmer, C.E.4
  • 178
    • 84864755176 scopus 로고    scopus 로고
    • Rewiring chemistry: algorithmic discovery and experimental validation of one-pot reactions in the network of organic chemistry
    • The Network of Chemistry is searched to identify combinations of reactions that can be carried out under the same conditions (1 pot) and this is validated by synthesizing a pharmaceutical requiring four sequential reactions (cyclization, chlorination, alkynylation, and arylation) in one setup.
    • Gothard CM, Soh S, Gothard NA, Kowalczyk B, Wei Y, Baytekin B, Grzybowski BA: Rewiring chemistry: algorithmic discovery and experimental validation of one-pot reactions in the network of organic chemistry. Angew Chem Int Ed 2012, 51:7922-7927.
    • (2012) Angew Chem Int Ed , vol.51 , pp. 7922-7927
    • Gothard, C.M.1    Soh, S.2    Gothard, N.A.3    Kowalczyk, B.4    Wei, Y.5    Baytekin, B.6    Grzybowski, B.A.7
  • 181
    • 85040105878 scopus 로고    scopus 로고
    • Computer-Assisted retrosynthesis based on molecular similarity
    • Single retrosynthetic steps are predicted using molecular similarity and it is shown that the reactants are in the top 10 predicted precursors 74.1% of the time. This approach does not require defining a reaction class.
    • Bogevig A, Federsel H-J, Huerta F, Hutchings MG, Kraut H, Langer T, Low P, Oppawsky C, Rein T, Saller H: Route Design in the 21st Century: The IC SYNTH Software Tool as an Idea Generator for Synthesis Prediction. Organic Process Research & Development 2015, 19:357-368.
    • (2017) ACS Cent Sci , vol.3 , pp. 1237-1245
    • Coley, C.W.1    Rogers, L.2    Green, W.H.3    Jensen, K.F.4
  • 183
    • 85065257848 scopus 로고    scopus 로고
    • Selection of cost-effective yet chemically diverse pathways from the networks of computer-generated retrosynthetic plans
    • Badowski, T., Molga, K., Grzybowski, B.A., Selection of cost-effective yet chemically diverse pathways from the networks of computer-generated retrosynthetic plans. Chem Sci 10 (2019), 4640–4651.
    • (2019) Chem Sci , vol.10 , pp. 4640-4651
    • Badowski, T.1    Molga, K.2    Grzybowski, B.A.3
  • 184
    • 85060049716 scopus 로고    scopus 로고
    • Navigating around patented routes by preserving specific motifs along computer-planned retrosynthetic pathways
    • The Chematica algorithm is modified to identify alternative modes of synthesis for the blockbuster and well patent protected pharmaceuticals linezolid, sitagliptin, and panobinostat.
    • Badowski T, Molga K, Grzybowski BA: Selection of cost-effective yet chemically diverse pathways from the networks of computer-generated retrosynthetic plans. Chemical Science 2019.
    • (2019) Chem , vol.5 , pp. 460-473
    • Molga, K.1    Dittwald, P.2    Grzybowski, B.A.3
  • 185
    • 85026897727 scopus 로고    scopus 로고
    • Towards automation of chemical process route selection based on data mining
    • Jacob, P.M., Yamin, P., Perez-Storey, C., Hopgood, M., Lapkin, A.A., Towards automation of chemical process route selection based on data mining. Green Chem 19 (2017), 140–152.
    • (2017) Green Chem , vol.19 , pp. 140-152
    • Jacob, P.M.1    Yamin, P.2    Perez-Storey, C.3    Hopgood, M.4    Lapkin, A.A.5
  • 187
    • 85047224318 scopus 로고    scopus 로고
    • A review of computational tools for design and reconstruction of metabolic pathways
    • Wang, L., Dash, S., Ng, C.Y., Maranas, C.D., A review of computational tools for design and reconstruction of metabolic pathways. Synth Sys Biotechnol 2 (2017), 243–252.
    • (2017) Synth Sys Biotechnol , vol.2 , pp. 243-252
    • Wang, L.1    Dash, S.2    Ng, C.Y.3    Maranas, C.D.4
  • 189
    • 84930203318 scopus 로고    scopus 로고
    • Orthogonal tandem catalysis
    • Lohr, T.L., Marks, T.J., Orthogonal tandem catalysis. Nat Chem, 7, 2015, 477.
    • (2015) Nat Chem , vol.7 , pp. 477
    • Lohr, T.L.1    Marks, T.J.2
  • 192
    • 84857192122 scopus 로고    scopus 로고
    • Computational tools for the synthetic design of biochemical pathways
    • Medema, M.H., Van Raaphorst, R., Takano, E., Breitling, R., Computational tools for the synthetic design of biochemical pathways. Nat Rev Microbiol 10 (2012), 191–202.
    • (2012) Nat Rev Microbiol , vol.10 , pp. 191-202
    • Medema, M.H.1    Van Raaphorst, R.2    Takano, E.3    Breitling, R.4
  • 193
    • 85029502961 scopus 로고    scopus 로고
    • A review of parameters and heuristics for guiding metabolic pathfinding
    • Kim, S.M., Peña, M.I., Moll, M., Bennett, G.N., Kavraki, L.E., A review of parameters and heuristics for guiding metabolic pathfinding. J Cheminf 9 (2017), 1–13.
    • (2017) J Cheminf , vol.9 , pp. 1-13
    • Kim, S.M.1    Peña, M.I.2    Moll, M.3    Bennett, G.N.4    Kavraki, L.E.5
  • 194
    • 85045712510 scopus 로고    scopus 로고
    • A pathway for every product? Tools to discover and design plant metabolism
    • Jeffryes, J.G., Seaver, S.M.D., Faria, J.P., Henry, C.S., A pathway for every product? Tools to discover and design plant metabolism. Plant Sci 273 (2018), 61–70.
    • (2018) Plant Sci , vol.273 , pp. 61-70
    • Jeffryes, J.G.1    Seaver, S.M.D.2    Faria, J.P.3    Henry, C.S.4
  • 198
    • 85049362552 scopus 로고    scopus 로고
    • Enumerating all possible biosynthetic pathways in metabolic networks
    • Ravikrishnan, A., Nasre, M., Raman, K., Enumerating all possible biosynthetic pathways in metabolic networks. Sci Rep, 8, 2018, 9932.
    • (2018) Sci Rep , vol.8 , pp. 9932
    • Ravikrishnan, A.1    Nasre, M.2    Raman, K.3
  • 199
    • 23144466440 scopus 로고    scopus 로고
    • Metabolic PathFinding: inferring relevant pathways in biochemical networks
    • Croes, D., Couche, F., van Helden, J., Wodak, S.J., Metabolic PathFinding: inferring relevant pathways in biochemical networks. Nucleic Acids Res 33 (2005), W326–W330.
    • (2005) Nucleic Acids Res , vol.33 , pp. W326-W330
    • Croes, D.1    Couche, F.2    van Helden, J.3    Wodak, S.J.4
  • 200
    • 64449087758 scopus 로고    scopus 로고
    • Metabolic pathfinding using RPAIR annotation
    • Faust, K., Croes, D., van Helden, J., Metabolic pathfinding using RPAIR annotation. J Mol Biol 388 (2009), 390–414.
    • (2009) J Mol Biol , vol.388 , pp. 390-414
    • Faust, K.1    Croes, D.2    van Helden, J.3
  • 201
    • 51749088153 scopus 로고    scopus 로고
    • MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization
    • Kohlbacher, O., Blum, T., MetaRoute: fast search for relevant metabolic routes for interactive network navigation and visualization. Bioinformatics 24 (2008), 2108–2109.
    • (2008) Bioinformatics , vol.24 , pp. 2108-2109
    • Kohlbacher, O.1    Blum, T.2
  • 202
    • 67849083088 scopus 로고    scopus 로고
    • FMM: a web server for metabolic pathway reconstruction and comparative analysis
    • Chou, C.-H., Chang, W.-C., Chiu, C.-M., Huang, C.-C., Huang, H.-D., FMM: a web server for metabolic pathway reconstruction and comparative analysis. Nucleic Acids Res 37 (2009), W129–W134.
    • (2009) Nucleic Acids Res , vol.37 , pp. W129-W134
    • Chou, C.-H.1    Chang, W.-C.2    Chiu, C.-M.3    Huang, C.-C.4    Huang, H.-D.5
  • 203
    • 0033670135 scopus 로고    scopus 로고
    • Pathway analysis in metabolic databases via differential metabolic display (DMD)
    • Küffner, R., Zimmer, R., Lengauer, T., Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics 16 (2000), 825–836.
    • (2000) Bioinformatics , vol.16 , pp. 825-836
    • Küffner, R.1    Zimmer, R.2    Lengauer, T.3
  • 204
    • 84898629889 scopus 로고    scopus 로고
    • Integer programming-based method for designing synthetic metabolic networks by minimum reaction insertion in a boolean model
    • Lu, W., Tamura, T., Song, J., Akutsu, T., Integer programming-based method for designing synthetic metabolic networks by minimum reaction insertion in a boolean model. PLoS One, 9, 2014, e92637.
    • (2014) PLoS One , vol.9 , pp. e92637
    • Lu, W.1    Tamura, T.2    Song, J.3    Akutsu, T.4
  • 205
    • 79957473580 scopus 로고    scopus 로고
    • Path finding methods accounting for stoichiometry in metabolic networks
    • Pey, J., Prada, J., Beasley, J.E., Planes, F.J., Path finding methods accounting for stoichiometry in metabolic networks. Genome Biol, 12, 2011, R49.
    • (2011) Genome Biol , vol.12 , pp. R49
    • Pey, J.1    Prada, J.2    Beasley, J.E.3    Planes, F.J.4
  • 206
    • 84910130469 scopus 로고    scopus 로고
    • Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering
    • The Chematica algorithm is modified to identify alternative modes of synthesis for the blockbuster and well patent protected pharmaceuticals linezolid, sitagliptin, and panobinostat.
    • Pey J, Prada J, Beasley JE, Planes FJ: Path finding methods accounting for stoichiometry in metabolic networks. Genome Biology 2011, 12:R49.
    • (2014) Biotechnol J , vol.9 , pp. 1446-1457
    • Fehér, T.1    Planson, A.G.2    Carbonell, P.3    Fernández-Castané, A.4    Grigoras, I.5    Dariy, E.6    Perret, A.7    Faulon, J.L.8
  • 207
    • 84897049113 scopus 로고    scopus 로고
    • Combining chemoinformatics with bioinformatics: in silico prediction of bacterial flavor-forming pathways by a chemical systems biology approach “reverse pathway engineering”
    • Liu, M., Bienfait, B., Sacher, O., Gasteiger, J., Siezen, R.J., Nauta, A., Geurts, J.M.W., Combining chemoinformatics with bioinformatics: in silico prediction of bacterial flavor-forming pathways by a chemical systems biology approach “reverse pathway engineering”. PLoS One, 9, 2014, e84769.
    • (2014) PLoS One , vol.9 , pp. e84769
    • Liu, M.1    Bienfait, B.2    Sacher, O.3    Gasteiger, J.4    Siezen, R.J.5    Nauta, A.6    Geurts, J.M.W.7
  • 208
    • 79961116083 scopus 로고    scopus 로고
    • A retrosynthetic biology approach to metabolic pathway design for therapeutic production
    • 122-122
    • Carbonell, P., Planson, A.-G., Fichera, D., Faulon, J.-L., A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Syst Biol, 5, 2011 122-122.
    • (2011) BMC Syst Biol , vol.5
    • Carbonell, P.1    Planson, A.-G.2    Fichera, D.3    Faulon, J.-L.4
  • 210
    • 84878862372 scopus 로고    scopus 로고
    • Metabolic tinker: an online tool for guiding the design of synthetic metabolic pathways
    • e113-e113 A thermodynamics-driven algorithm is developed to search the Universal Reaction Network for paths between any two metabolites.
    • Carbonell P, Parutto P, Herisson J, Pandit SB, Faulon J-L: XTMS: pathway design in an eXTended metabolic space. Nucleic Acids Research 2014, 42:W389-W394.
    • (2013) Nucleic Acids Res , vol.41
    • McClymont, K.1    Soyer, O.S.2
  • 211
    • 84856579358 scopus 로고    scopus 로고
    • Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms
    • Carbonell, P., Fichera, D., Pandit, S.B., Faulon, J.-L., Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. BMC Syst Biol, 6, 2012, 10.
    • (2012) BMC Syst Biol , vol.6 , pp. 10
    • Carbonell, P.1    Fichera, D.2    Pandit, S.B.3    Faulon, J.-L.4
  • 213
    • 85038207858 scopus 로고    scopus 로고
    • RetroPath2.0: A retrosynthesis workflow for metabolic engineers
    • Reaction rules are encoded as SMIRK-like strings. The program provides solutions to different tasks given the rules, source compounds, and sink compounds, such as designing new pathway to a molecule and biosensor development.
    • Carbonell P, Fichera D, Pandit SB, Faulon J-L: Enumerating metabolic pathways for the production of heterologous target chemicals in chassis organisms. BMC Systems Biology 2012, 6:10.
    • (2018) Metab Eng , vol.45 , pp. 158-170
    • Delépine, B.1    Duigou, T.2    Carbonell, P.3    Faulon, J.L.4
  • 215
    • 85043307792 scopus 로고    scopus 로고
    • Pathway design using de novo steps through uncharted biochemical spaces
    • 184-184 The rePrime and novoStoic algorithms are described for rule extraction and mass-balanced path optimization, respectively.
    • Kumar A, Wang L, Ng CY, Maranas CD: Pathway design using de novo steps through uncharted biochemical spaces. Nat Commun 2018, 9:184-184.
    • (2018) Nat Commun , vol.9
    • Kumar, A.1    Wang, L.2    Ng, C.Y.3    Maranas, C.D.4
  • 217
    • 85020239251 scopus 로고    scopus 로고
    • ReactPRED: a tool to predict and analyze biochemical reactions
    • Sivakumar, T.V., Giri, V., Park, J.H., Kim, T.Y., Bhaduri, A., ReactPRED: a tool to predict and analyze biochemical reactions. Bioinformatics 32 (2016), 3522–3524.
    • (2016) Bioinformatics , vol.32 , pp. 3522-3524
    • Sivakumar, T.V.1    Giri, V.2    Park, J.H.3    Kim, T.Y.4    Bhaduri, A.5
  • 218
    • 84899702032 scopus 로고    scopus 로고
    • RetroRules: a database of reaction rules for engineering biology
    • A publicly accessible database of 400,000 + reaction rules accounting for stereochemistry and provided for different distances from the reaction center.
    • Carbonell P, Parutto P, Baudier C, Junot C, Faulon JL: Retropath: Automated pipeline for embedded metabolic circuits. ACS Synthetic Biology 2014, 3:565-577.
    • (2018) Nucleic Acids Res , pp. 1-7
    • Duigou, T.1    du Lac, M.2    Carbonell, P.3    Faulon, J.-L.4
  • 219
    • 79959955242 scopus 로고    scopus 로고
    • The university of Minnesota pathway prediction system: multi-level prediction and visualization
    • Gao, J., Wackett, L.P., Ellis, L.B.M., The university of Minnesota pathway prediction system: multi-level prediction and visualization. Nucleic Acids Res 39 (2011), W406–W411.
    • (2011) Nucleic Acids Res , vol.39 , pp. W406-W411
    • Gao, J.1    Wackett, L.P.2    Ellis, L.B.M.3
  • 220
    • 84993958585 scopus 로고    scopus 로고
    • ATLAS of biochemistry: a repository of all possible biochemical reactions for synthetic biology and metabolic engineering studies
    • A publicly available database of metabolites and reactions enumerated based on simple reaction rules.
    • Hadadi N, Hafner J, Shajkofci A, Zisaki A, Hatzimanikatis V: ATLAS of biochemistry: a repository of all possible biochemical reactions for synthetic biology and metabolic engineering studies. ACS Synth Biol 2016, 5:1155-1166.
    • (2016) ACS Synth Biol , vol.5 , pp. 1155-1166
    • Hadadi, N.1    Hafner, J.2    Shajkofci, A.3    Zisaki, A.4    Hatzimanikatis, V.5
  • 221
    • 34547691000 scopus 로고    scopus 로고
    • Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways
    • Oh, M., Yamada, T., Hattori, M., Goto, S., Kanehisa, M., Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. J Chem Inf Model 47 (2007), 1702–1712.
    • (2007) J Chem Inf Model , vol.47 , pp. 1702-1712
    • Oh, M.1    Yamada, T.2    Hattori, M.3    Goto, S.4    Kanehisa, M.5
  • 222
    • 0028534521 scopus 로고
    • Meta. 1. A program for the evaluation of metabolic transformation of chemicals
    • Klopman, G., Dimayuga, M., Talafous, J., Meta. 1. A program for the evaluation of metabolic transformation of chemicals. J Chem Inf Comput Sci 34 (1994), 1320–1325.
    • (1994) J Chem Inf Comput Sci , vol.34 , pp. 1320-1325
    • Klopman, G.1    Dimayuga, M.2    Talafous, J.3
  • 223
    • 0028534522 scopus 로고
    • Meta. 2. A dictionary model of mammalian xenobiotic metabolism
    • Talafous, J., Sayre, L.M., Mieyal, J.J., Klopman, G., Meta. 2. A dictionary model of mammalian xenobiotic metabolism. J Chem Inf Comput Sci 34 (1994), 1326–1333.
    • (1994) J Chem Inf Comput Sci , vol.34 , pp. 1326-1333
    • Talafous, J.1    Sayre, L.M.2    Mieyal, J.J.3    Klopman, G.4
  • 224
    • 4344685196 scopus 로고    scopus 로고
    • Encoding microbial metabolic logic: predicting biodegradation
    • Hou, B.K., Ellis, L.B.M., Wackett, L.P., Encoding microbial metabolic logic: predicting biodegradation. J Ind Microbiol Biotechnol 31 (2004), 261–272.
    • (2004) J Ind Microbiol Biotechnol , vol.31 , pp. 261-272
    • Hou, B.K.1    Ellis, L.B.M.2    Wackett, L.P.3
  • 225
    • 33644877427 scopus 로고    scopus 로고
    • The university of Minnesota biocatalysis/biodegradation database: the first decade
    • Ellis, L.B.M., Roe, D., Wackett, L.P., The university of Minnesota biocatalysis/biodegradation database: the first decade. Nucleic Acids Res 34 (2006), D517–D521.
    • (2006) Nucleic Acids Res , vol.34 , pp. D517-D521
    • Ellis, L.B.M.1    Roe, D.2    Wackett, L.P.3
  • 226
    • 84929143779 scopus 로고    scopus 로고
    • Efficient searching and annotation of metabolic networks using chemical similarity
    • Stine, A.E., Pertusi, D.A., Tyo, K.E.J., Broadbelt, L.J., Efficient searching and annotation of metabolic networks using chemical similarity. Bioinformatics 31 (2014), 1016–1024.
    • (2014) Bioinformatics , vol.31 , pp. 1016-1024
    • Stine, A.E.1    Pertusi, D.A.2    Tyo, K.E.J.3    Broadbelt, L.J.4
  • 227
    • 84936966835 scopus 로고    scopus 로고
    • Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways
    • Hadadi, N., Hatzimanikatis, V., Design of computational retrobiosynthesis tools for the design of de novo synthetic pathways. Curr Opin Chem Biol 28 (2015), 99–104.
    • (2015) Curr Opin Chem Biol , vol.28 , pp. 99-104
    • Hadadi, N.1    Hatzimanikatis, V.2
  • 228
    • 75949089439 scopus 로고    scopus 로고
    • Automatic assignment of reaction operators to enzymatic reactions
    • Schomburg, D., Schomburg, I., Leber, M., Egelhofer, V., Automatic assignment of reaction operators to enzymatic reactions. Bioinformatics 25 (2009), 3135–3142.
    • (2009) Bioinformatics , vol.25 , pp. 3135-3142
    • Schomburg, D.1    Schomburg, I.2    Leber, M.3    Egelhofer, V.4
  • 229
    • 77953329895 scopus 로고    scopus 로고
    • Prediction of novel synthetic pathways for the production of desired chemicals
    • Cho, A., Yun, H., Park, J.H., Lee, S.Y., Park, S., Prediction of novel synthetic pathways for the production of desired chemicals. BMC Syst Biol, 4, 2010, 35.
    • (2010) BMC Syst Biol , vol.4 , pp. 35
    • Cho, A.1    Yun, H.2    Park, J.H.3    Lee, S.Y.4    Park, S.5
  • 231
    • 22744439567 scopus 로고    scopus 로고
    • The evolution of connectivity in metabolic networks
    • Pfeiffer, T., Soyer, O.S., Bonhoeffer, S., The evolution of connectivity in metabolic networks. PLoS Biol, 3, 2005, e228.
    • (2005) PLoS Biol , vol.3 , pp. e228
    • Pfeiffer, T.1    Soyer, O.S.2    Bonhoeffer, S.3
  • 232
    • 77953578214 scopus 로고    scopus 로고
    • Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate
    • Henry, C.S., Broadbelt, L.J., Hatzimanikatis, V., Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate. Biotechnol Bioeng 106 (2010), 462–473.
    • (2010) Biotechnol Bioeng , vol.106 , pp. 462-473
    • Henry, C.S.1    Broadbelt, L.J.2    Hatzimanikatis, V.3
  • 233
    • 84958290345 scopus 로고    scopus 로고
    • MapMaker and PathTracer for tracking carbon in genome-scale metabolic models
    • Tervo, C.J., Reed, J.L., MapMaker and PathTracer for tracking carbon in genome-scale metabolic models. Biotechnol J 11 (2016), 648–661.
    • (2016) Biotechnol J , vol.11 , pp. 648-661
    • Tervo, C.J.1    Reed, J.L.2
  • 234
    • 85009103532 scopus 로고    scopus 로고
    • A method for finding metabolic pathways using atomic group tracking
    • e0168725-e0168725
    • Huang, Y., Zhong, C., Lin, H.X., Wang, J., A method for finding metabolic pathways using atomic group tracking. PLoS One, 12, 2017 e0168725-e0168725.
    • (2017) PLoS One , vol.12
    • Huang, Y.1    Zhong, C.2    Lin, H.X.3    Wang, J.4
  • 235
    • 84903954626 scopus 로고    scopus 로고
    • Optimal metabolic route search based on atom mappings
    • Latendresse, M., Krummenacker, M., Karp, P.D., Optimal metabolic route search based on atom mappings. Bioinformatics 30 (2014), 2043–2050.
    • (2014) Bioinformatics , vol.30 , pp. 2043-2050
    • Latendresse, M.1    Krummenacker, M.2    Karp, P.D.3
  • 236
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: understanding the cell's functional organization
    • Barabási, A.-L., Oltvai, Z.N., Network biology: understanding the cell's functional organization. Nat Rev Genet 5 (2004), 101–113.
    • (2004) Nat Rev Genet , vol.5 , pp. 101-113
    • Barabási, A.-L.1    Oltvai, Z.N.2
  • 237
    • 70749083404 scopus 로고    scopus 로고
    • Inferring branching pathways in genome-scale metabolic networks
    • Pitkänen, E., Jouhten, P., Rousu, J., Inferring branching pathways in genome-scale metabolic networks. BMC Syst Biol 3 (2009), 1–22.
    • (2009) BMC Syst Biol , vol.3 , pp. 1-22
    • Pitkänen, E.1    Jouhten, P.2    Rousu, J.3
  • 238
    • 84880781653 scopus 로고    scopus 로고
    • Consistent estimation of Gibbs energy using component contributions
    • Noor, E., Haraldsdóttir, H.S., Milo, R., Fleming, R.M.T., Consistent estimation of Gibbs energy using component contributions. PLoS Comput Biol, 9, 2013, e1003098.
    • (2013) PLoS Comput Biol , vol.9 , pp. e1003098
    • Noor, E.1    Haraldsdóttir, H.S.2    Milo, R.3    Fleming, R.M.T.4
  • 239
    • 84946594571 scopus 로고    scopus 로고
    • Designing overall stoichiometric conversions and intervening metabolic reactions
    • Chowdhury, A., Maranas, C.D., Designing overall stoichiometric conversions and intervening metabolic reactions. Sci Rep, 5, 2015, 16009.
    • (2015) Sci Rep , vol.5 , pp. 16009
    • Chowdhury, A.1    Maranas, C.D.2
  • 240
    • 84921803508 scopus 로고    scopus 로고
    • FindPath: a Matlab solution for in silico design of synthetic metabolic pathways
    • Vieira, G., Portais, J.-C., Carnicer, M., Heux, S., FindPath: a Matlab solution for in silico design of synthetic metabolic pathways. Bioinformatics 30 (2014), 2986–2988.
    • (2014) Bioinformatics , vol.30 , pp. 2986-2988
    • Vieira, G.1    Portais, J.-C.2    Carnicer, M.3    Heux, S.4
  • 241
    • 84861429699 scopus 로고    scopus 로고
    • eQuilibrator—the biochemical thermodynamics calculator
    • The authors provide a database and automated interface for estimating the Gibbs free energy of formation for biomolecules based on decades of empirical data.
    • Chowdhury A, Maranas CD: Designing overall stoichiometric conversions and intervening metabolic reactions. Scientific Reports 2015, 5:16009.
    • (2011) Nucleic Acids Res , vol.40 , pp. D770-D775
    • Bar-Even, A.1    Flamholz, A.2    Noor, E.3    Milo, R.4
  • 242
    • 84865136870 scopus 로고    scopus 로고
    • An integrated open framework for thermodynamics of reactions that combines accuracy and coverage
    • Bar-Even, A., Flamholz, A., Davidi, D., Noor, E., Milo, R., Lubling, Y., An integrated open framework for thermodynamics of reactions that combines accuracy and coverage. Bioinformatics 28 (2012), 2037–2044.
    • (2012) Bioinformatics , vol.28 , pp. 2037-2044
    • Bar-Even, A.1    Flamholz, A.2    Davidi, D.3    Noor, E.4    Milo, R.5    Lubling, Y.6
  • 243
    • 84895727036 scopus 로고    scopus 로고
    • Pathway thermodynamics highlights kinetic obstacles in central metabolism
    • Using the TCA cycle as an example, the authors assess the utility of thermodynamic calculations in evaluating pathway fitness.
    • Noor E, Bar-Even A, Flamholz A, Reznik E, Liebermeister W, Milo R: Pathway thermodynamics highlights kinetic obstacles in central metabolism. PLoS Comput Biol 2014, 10:e1003483.
    • (2014) PLoS Comput Biol , vol.10 , pp. e1003483
    • Noor, E.1    Bar-Even, A.2    Flamholz, A.3    Reznik, E.4    Liebermeister, W.5    Milo, R.6
  • 244
    • 84855946759 scopus 로고    scopus 로고
    • Compound toxicity screening and structure–activity relationship modeling in Escherichia coli
    • Planson, A.-G., Carbonell, P., Paillard, E., Pollet, N., Faulon, J.-L., Compound toxicity screening and structure–activity relationship modeling in Escherichia coli. Biotechnol Bioeng 109 (2012), 846–850.
    • (2012) Biotechnol Bioeng , vol.109 , pp. 846-850
    • Planson, A.-G.1    Carbonell, P.2    Paillard, E.3    Pollet, N.4    Faulon, J.-L.5
  • 245
    • 0242712386 scopus 로고    scopus 로고
    • Applicability and limitation of QSARs for the toxicity of electrophilic chemicals
    • Harder, A., Escher, B.I., Schwarzenbach, R.P., Applicability and limitation of QSARs for the toxicity of electrophilic chemicals. Environ Sci Technol 37 (2003), 4955–4961.
    • (2003) Environ Sci Technol , vol.37 , pp. 4955-4961
    • Harder, A.1    Escher, B.I.2    Schwarzenbach, R.P.3
  • 247
    • 54949140438 scopus 로고    scopus 로고
    • DESHARKY: automatic design of metabolic pathways for optimal cell growth
    • Rodrigo, G., Jaramillo, A., Carrera, J., Prather, K.J., DESHARKY: automatic design of metabolic pathways for optimal cell growth. Bioinformatics 24 (2008), 2554–2556.
    • (2008) Bioinformatics , vol.24 , pp. 2554-2556
    • Rodrigo, G.1    Jaramillo, A.2    Carrera, J.3    Prather, K.J.4
  • 248
    • 84961778425 scopus 로고    scopus 로고
    • Biocatalysis: successfully crossing boundaries
    • Bornscheuer, U.T., Biocatalysis: successfully crossing boundaries. Angew Chem Int Ed 55 (2016), 4372–4373.
    • (2016) Angew Chem Int Ed , vol.55 , pp. 4372-4373
    • Bornscheuer, U.T.1
  • 249
    • 85021333805 scopus 로고    scopus 로고
    • Enantioselective chemo- and biocatalysis: partners in retrosynthesis
    • Hönig, M., Sondermann, P., Turner, N.J., Carreira, E.M., Enantioselective chemo- and biocatalysis: partners in retrosynthesis. Angew Chem Int Ed 56 (2017), 8942–8973.
    • (2017) Angew Chem Int Ed , vol.56 , pp. 8942-8973
    • Hönig, M.1    Sondermann, P.2    Turner, N.J.3    Carreira, E.M.4
  • 250
    • 84956924903 scopus 로고    scopus 로고
    • Directed evolution of enzymes for industrial biocatalysis
    • Porter, J.L., Rusli, R.A., Ollis, D.L., Directed evolution of enzymes for industrial biocatalysis. Chembiochem 17 (2016), 197–203.
    • (2016) Chembiochem , vol.17 , pp. 197-203
    • Porter, J.L.1    Rusli, R.A.2    Ollis, D.L.3
  • 251
    • 84947611961 scopus 로고    scopus 로고
    • Industrial applications of enzyme biocatalysis: current status and future aspects
    • Choi, J.-M., Han, S.-S., Kim, H.-S., Industrial applications of enzyme biocatalysis: current status and future aspects. Biotechnol Adv 33 (2015), 1443–1454.
    • (2015) Biotechnol Adv , vol.33 , pp. 1443-1454
    • Choi, J.-M.1    Han, S.-S.2    Kim, H.-S.3
  • 252
    • 85019690346 scopus 로고    scopus 로고
    • Constructing biocatalytic cascades: in vitro and in vivo approaches to de Novo multi-enzyme pathways
    • France, S.P., Hepworth, L.J., Turner, N.J., Flitsch, S.L., Constructing biocatalytic cascades: in vitro and in vivo approaches to de Novo multi-enzyme pathways. ACS Catal 7 (2017), 710–724.
    • (2017) ACS Catal , vol.7 , pp. 710-724
    • France, S.P.1    Hepworth, L.J.2    Turner, N.J.3    Flitsch, S.L.4
  • 253
    • 85006197272 scopus 로고    scopus 로고
    • Microbial enzymes: industrial progress in 21st century
    • Singh, R., Kumar, M., Mittal, A., Mehta, P.K., Microbial enzymes: industrial progress in 21st century. 3 Biotech, 6, 2016, 174.
    • (2016) 3 Biotech , vol.6 , pp. 174
    • Singh, R.1    Kumar, M.2    Mittal, A.3    Mehta, P.K.4
  • 256
    • 85048243784 scopus 로고    scopus 로고
    • Industrial applications of enzymes: recent advances, techniques, and outlooks
    • Chapman, J., Ismail, E.A., Dinu, Z.C., Industrial applications of enzymes: recent advances, techniques, and outlooks. Catalysts, 8, 2018.
    • (2018) Catalysts , vol.8
    • Chapman, J.1    Ismail, E.A.2    Dinu, Z.C.3
  • 258
    • 85041205932 scopus 로고    scopus 로고
    • Remote C-H hydroxylation by an α-ketoglutarate-dependent dioxygenase enables efficient chemoenzymatic synthesis of manzacidin C and proline analogs
    • Zwick, C.R., Renata, H., Remote C-H hydroxylation by an α-ketoglutarate-dependent dioxygenase enables efficient chemoenzymatic synthesis of manzacidin C and proline analogs. J Am Chem Soc 140 (2018), 1165–1169.
    • (2018) J Am Chem Soc , vol.140 , pp. 1165-1169
    • Zwick, C.R.1    Renata, H.2
  • 260
    • 84973364522 scopus 로고    scopus 로고
    • From a sequential to a concurrent reaction in aqueous medium: ruthenium-catalyzed allylic alcohol isomerization and asymmetric bioreduction
    • Ríos-Lombardía, N., Vidal, C., Liardo, E., Morís, F., García-Álvarez, J., González-Sabín, J., From a sequential to a concurrent reaction in aqueous medium: ruthenium-catalyzed allylic alcohol isomerization and asymmetric bioreduction. Angew Chem Int Ed 55 (2016), 8691–8695.
    • (2016) Angew Chem Int Ed , vol.55 , pp. 8691-8695
    • Ríos-Lombardía, N.1    Vidal, C.2    Liardo, E.3    Morís, F.4    García-Álvarez, J.5    González-Sabín, J.6
  • 262
    • 84940651102 scopus 로고    scopus 로고
    • Vinylation of unprotected phenols using a biocatalytic system
    • Busto, E., Simon, R.C., Kroutil, W., Vinylation of unprotected phenols using a biocatalytic system. Angew Chem Int Ed 54 (2015), 10899–10902.
    • (2015) Angew Chem Int Ed , vol.54 , pp. 10899-10902
    • Busto, E.1    Simon, R.C.2    Kroutil, W.3
  • 263
    • 84874256566 scopus 로고    scopus 로고
    • Multistep enzymatic synthesis of long-chain α,ω-dicarboxylic and ω-hydroxycarboxylic acids from renewable fatty acids and plant oils
    • Song, J.-W., Jeon, E.-Y., Song, D.-H., Jang, H.-Y., Bornscheuer, U.T., Oh, D.-K., Park, J.-B., Multistep enzymatic synthesis of long-chain α,ω-dicarboxylic and ω-hydroxycarboxylic acids from renewable fatty acids and plant oils. Angew Chem Int Ed 52 (2013), 2534–2537.
    • (2013) Angew Chem Int Ed , vol.52 , pp. 2534-2537
    • Song, J.-W.1    Jeon, E.-Y.2    Song, D.-H.3    Jang, H.-Y.4    Bornscheuer, U.T.5    Oh, D.-K.6    Park, J.-B.7
  • 267
    • 85010676738 scopus 로고    scopus 로고
    • Programmable genome editing tools and their regulation for efficient genome engineering
    • Guha, T.K., Wai, A., Hausner, G., Programmable genome editing tools and their regulation for efficient genome engineering. Comput Struct Biotechnol J 15 (2017), 146–160.
    • (2017) Comput Struct Biotechnol J , vol.15 , pp. 146-160
    • Guha, T.K.1    Wai, A.2    Hausner, G.3
  • 268
    • 85034250678 scopus 로고    scopus 로고
    • Development of a CRISPR/Cas9 genome editing toolbox for Corynebacterium glutamicum
    • Liu, J., Wang, Y., Lu, Y., Zheng, P., Sun, J., Ma, Y., Development of a CRISPR/Cas9 genome editing toolbox for Corynebacterium glutamicum. Microb Cell Factories 16 (2017), 1–17.
    • (2017) Microb Cell Factories , vol.16 , pp. 1-17
    • Liu, J.1    Wang, Y.2    Lu, Y.3    Zheng, P.4    Sun, J.5    Ma, Y.6
  • 270
    • 85044589051 scopus 로고    scopus 로고
    • CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms
    • Shapiro, R.S., Chavez, A., Collins, J.J., CRISPR-based genomic tools for the manipulation of genetically intractable microorganisms. Nat Rev Microbiol 16 (2018), 333–339.
    • (2018) Nat Rev Microbiol , vol.16 , pp. 333-339
    • Shapiro, R.S.1    Chavez, A.2    Collins, J.J.3
  • 271
    • 85045117799 scopus 로고    scopus 로고
    • Applications of CRISPR/cas system to bacterial metabolic engineering
    • Cho, S., Shin, J., Cho, B.-K., Applications of CRISPR/cas system to bacterial metabolic engineering. Int J Mol Sci, 19, 2018.
    • (2018) Int J Mol Sci , vol.19
    • Cho, S.1    Shin, J.2    Cho, B.-K.3
  • 273
    • 84934947770 scopus 로고    scopus 로고
    • High-Efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/cas system
    • Cobb, R.E., Wang, Y., Zhao, H., High-Efficiency multiplex genome editing of Streptomyces species using an engineered CRISPR/cas system. ACS Synth Biol 4 (2015), 723–728.
    • (2015) ACS Synth Biol , vol.4 , pp. 723-728
    • Cobb, R.E.1    Wang, Y.2    Zhao, H.3
  • 274
    • 84892459952 scopus 로고    scopus 로고
    • A vector library for silencing central carbon metabolism genes with antisense RNAs in escherichia coli
    • Nakashima, N., Ohno, S., Yoshikawa, K., Shimizu, H., Tamura, T., A vector library for silencing central carbon metabolism genes with antisense RNAs in escherichia coli. Appl Environ Microbiol 80 (2014), 564–573.
    • (2014) Appl Environ Microbiol , vol.80 , pp. 564-573
    • Nakashima, N.1    Ohno, S.2    Yoshikawa, K.3    Shimizu, H.4    Tamura, T.5
  • 275
    • 84930227327 scopus 로고    scopus 로고
    • Using genome-scale models to predict biological capabilities
    • O'Brien Edward, J., Monk Jonathan, M., Palsson Bernhard, O., Using genome-scale models to predict biological capabilities. Cell 161 (2015), 971–987.
    • (2015) Cell , vol.161 , pp. 971-987
    • O'Brien Edward, J.1    Monk Jonathan, M.2    Palsson Bernhard, O.3
  • 276
    • 84895756673 scopus 로고    scopus 로고
    • Integrating kinetics with flux balance analysis for strain design
    • Chowdhury, A., Zomorrodi, A.R., Maranas, C.D., OptForce, k-, Integrating kinetics with flux balance analysis for strain design. PLoS Comput Biol, 10, 2014, e1003487.
    • (2014) PLoS Comput Biol , vol.10 , pp. e1003487
    • Chowdhury, A.1    Zomorrodi, A.R.2    Maranas, C.D.3    OptForce, K.4
  • 277
    • 85052688100 scopus 로고    scopus 로고
    • Metabolic engineering of Escherichia coli for the enhanced production of l-tyrosine
    • Kim, B., Binkley, R., Kim, H.U., Lee, S.Y., Metabolic engineering of Escherichia coli for the enhanced production of l-tyrosine. Biotechnol Bioeng 115 (2018), 2554–2564.
    • (2018) Biotechnol Bioeng , vol.115 , pp. 2554-2564
    • Kim, B.1    Binkley, R.2    Kim, H.U.3    Lee, S.Y.4
  • 278
    • 85031815634 scopus 로고    scopus 로고
    • Metabolism of the fast-growing bacterium Vibrio natriegens elucidated by 13C metabolic flux analysis
    • Long, C.P., Gonzalez, J.E., Cipolla, R.M., Antoniewicz, M.R., Metabolism of the fast-growing bacterium Vibrio natriegens elucidated by 13C metabolic flux analysis. Metab Eng 44 (2017), 191–197.
    • (2017) Metab Eng , vol.44 , pp. 191-197
    • Long, C.P.1    Gonzalez, J.E.2    Cipolla, R.M.3    Antoniewicz, M.R.4
  • 280
    • 85029539622 scopus 로고    scopus 로고
    • Multiplex genome editing by natural transformation (MuGENT) for synthetic biology in Vibrio natriegens
    • Dalia, T.N., Hayes, C.A., Stolyar, S., Marx, C.J., McKinlay, J.B., Dalia, A.B., Multiplex genome editing by natural transformation (MuGENT) for synthetic biology in Vibrio natriegens. ACS Synth Biol 6 (2017), 1650–1655.
    • (2017) ACS Synth Biol , vol.6 , pp. 1650-1655
    • Dalia, T.N.1    Hayes, C.A.2    Stolyar, S.3    Marx, C.J.4    McKinlay, J.B.5    Dalia, A.B.6
  • 281
    • 84899698094 scopus 로고    scopus 로고
    • Programming biological operating systems: genome design, assembly and activation
    • Gibson, D.G., Programming biological operating systems: genome design, assembly and activation. Nat Methods 11 (2014), 521–526.
    • (2014) Nat Methods , vol.11 , pp. 521-526
    • Gibson, D.G.1
  • 283
    • 77249153701 scopus 로고    scopus 로고
    • Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism
    • Komatsu, M., Uchiyama, T., Omura, S., Cane, D.E., Ikeda, H., Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. Proc Natl Acad Sci Unit States Am 107 (2010), 2646–2651.
    • (2010) Proc Natl Acad Sci Unit States Am , vol.107 , pp. 2646-2651
    • Komatsu, M.1    Uchiyama, T.2    Omura, S.3    Cane, D.E.4    Ikeda, H.5
  • 284
    • 79951846247 scopus 로고    scopus 로고
    • Engineering Streptomyces coelicolor for heterologous expression of secondary metabolite gene clusters
    • Gomez-Escribano, J.P., Bibb, M.J., Engineering Streptomyces coelicolor for heterologous expression of secondary metabolite gene clusters. Microb Biotechnol 4 (2011), 207–215.
    • (2011) Microb Biotechnol , vol.4 , pp. 207-215
    • Gomez-Escribano, J.P.1    Bibb, M.J.2
  • 288
    • 0034887171 scopus 로고    scopus 로고
    • Polyketide biosynthesis: a millennium review
    • Staunton, J., Weissman, K.J., Polyketide biosynthesis: a millennium review. Nat Prod Rep 18 (2001), 380–416.
    • (2001) Nat Prod Rep , vol.18 , pp. 380-416
    • Staunton, J.1    Weissman, K.J.2
  • 289
    • 84859643086 scopus 로고    scopus 로고
    • Combinatorial biosynthesis of polyketides—a perspective
    • Wong, F.T., Khosla, C., Combinatorial biosynthesis of polyketides—a perspective. Curr Opin Chem Biol 16 (2012), 117–123.
    • (2012) Curr Opin Chem Biol , vol.16 , pp. 117-123
    • Wong, F.T.1    Khosla, C.2
  • 290
    • 84900552743 scopus 로고    scopus 로고
    • Assembly line polyketide synthases: mechanistic insights and unsolved problems
    • Khosla, C., Herschlag, D., Cane, D.E., Walsh, C.T., Assembly line polyketide synthases: mechanistic insights and unsolved problems. Biochemistry 53 (2014), 2875–2883.
    • (2014) Biochemistry , vol.53 , pp. 2875-2883
    • Khosla, C.1    Herschlag, D.2    Cane, D.E.3    Walsh, C.T.4
  • 291
    • 85054968290 scopus 로고    scopus 로고
    • Engineering strategies for rational polyketide synthase design
    • Klaus, M., Grininger, M., Engineering strategies for rational polyketide synthase design. Nat Prod Rep 35 (2018), 1070–1081.
    • (2018) Nat Prod Rep , vol.35 , pp. 1070-1081
    • Klaus, M.1    Grininger, M.2
  • 292
    • 84960811836 scopus 로고    scopus 로고
    • Two transcription factors, CabA and CabR, are independently involved in multilevel regulation of the biosynthetic gene cluster encoding the novel aminocoumarin, cacibiocin
    • Wolański, M., Łebkowski, T., Kois-Ostrowska, A., Zettler, J., Apel, A.K., Jakimowicz, D., Zakrzewska-Czerwińska, J., Two transcription factors, CabA and CabR, are independently involved in multilevel regulation of the biosynthetic gene cluster encoding the novel aminocoumarin, cacibiocin. Appl Microbiol Biotechnol 100 (2016), 3147–3164.
    • (2016) Appl Microbiol Biotechnol , vol.100 , pp. 3147-3164
    • Wolański, M.1    Łebkowski, T.2    Kois-Ostrowska, A.3    Zettler, J.4    Apel, A.K.5    Jakimowicz, D.6    Zakrzewska-Czerwińska, J.7
  • 294
    • 84892451203 scopus 로고    scopus 로고
    • A TetR family transcriptional regulator, coordinates the biosynthesis and export of gougerotin in Streptomyces graminearus
    • Wei, J., Tian, Y., Niu, G., Tan, H., GouR, A TetR family transcriptional regulator, coordinates the biosynthesis and export of gougerotin in Streptomyces graminearus. Appl Environ Microbiol 80 (2014), 714–722.
    • (2014) Appl Environ Microbiol , vol.80 , pp. 714-722
    • Wei, J.1    Tian, Y.2    Niu, G.3    Tan, H.4    GouR5
  • 295
    • 76649123602 scopus 로고    scopus 로고
    • Characterization and analysis of the regulatory network involved in control of lipomycin biosynthesis in Streptomyces aureofaciens Tü117
    • Horbal, L., Rebets, Y., Rabyk, M., Luzhetskyy, A., Ostash, B., Welle, E., Nakamura, T., Fedorenko, V., Bechthold, A., Characterization and analysis of the regulatory network involved in control of lipomycin biosynthesis in Streptomyces aureofaciens Tü117. Appl Microbiol Biotechnol 85 (2010), 1069–1079.
    • (2010) Appl Microbiol Biotechnol , vol.85 , pp. 1069-1079
    • Horbal, L.1    Rebets, Y.2    Rabyk, M.3    Luzhetskyy, A.4    Ostash, B.5    Welle, E.6    Nakamura, T.7    Fedorenko, V.8    Bechthold, A.9
  • 296
    • 85052701919 scopus 로고    scopus 로고
    • Metabolic engineering of microorganisms for the production of natural compounds
    • Park, S.Y., Yang, D., Ha, S.H., Lee, S.Y., Metabolic engineering of microorganisms for the production of natural compounds. Adv Biosys, 2, 2018, 1700190.
    • (2018) Adv Biosys , vol.2 , pp. 1700190
    • Park, S.Y.1    Yang, D.2    Ha, S.H.3    Lee, S.Y.4
  • 298
    • 84859633048 scopus 로고    scopus 로고
    • Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids
    • Zhang, F., Carothers, J.M., Keasling, J.D., Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 30 (2012), 354–359.
    • (2012) Nat Biotechnol , vol.30 , pp. 354-359
    • Zhang, F.1    Carothers, J.M.2    Keasling, J.D.3
  • 300
    • 85044313699 scopus 로고    scopus 로고
    • Layered dynamic regulation for improving metabolic pathway productivity in Escherichia coli
    • Doong, S.J., Gupta, A., Prather, K.L.J., Layered dynamic regulation for improving metabolic pathway productivity in Escherichia coli. Proc Natl Acad Sci Unit States Am 115 (2018), 2964–2969.
    • (2018) Proc Natl Acad Sci Unit States Am , vol.115 , pp. 2964-2969
    • Doong, S.J.1    Gupta, A.2    Prather, K.L.J.3
  • 302
    • 85054008896 scopus 로고    scopus 로고
    • Cellular checkpoint control using programmable sequential logic
    • Andrews, L.B., Nielsen, A.A.K., Voigt, C.A., Cellular checkpoint control using programmable sequential logic. Science, 361, 2018, eaap8987.
    • (2018) Science , vol.361 , pp. eaap8987
    • Andrews, L.B.1    Nielsen, A.A.K.2    Voigt, C.A.3
  • 303
    • 85044533667 scopus 로고    scopus 로고
    • A semi-synthetic regulon enables rapid growth of yeast on xylose
    • To overcome growth limitations by yeast on xylose, they create alternative Gal4 regulatory circuits that do not trigger the starvation response.
    • Venayak N, Anesiadis N, Cluett WR, Mahadevan R: Engineering metabolism through dynamic control. Current Opinion in Biotechnology 2015, 34:142-152.
    • (2018) Nat Commun , vol.9 , pp. 1233
    • Endalur Gopinarayanan, V.1    Nair, N.U.2
  • 304
    • 85021377734 scopus 로고    scopus 로고
    • An S: spatial organization of metabolic enzyme complexes in cells
    • Schmitt, D.L., An S: spatial organization of metabolic enzyme complexes in cells. Biochemistry 56 (2017), 3184–3196.
    • (2017) Biochemistry , vol.56 , pp. 3184-3196
    • Schmitt, D.L.1
  • 305
    • 30544434619 scopus 로고    scopus 로고
    • Combinatorial biosynthesis of reduced polyketides
    • Weissman, K.J., Leadlay, P.F., Combinatorial biosynthesis of reduced polyketides. Nat Rev Microbiol, 3, 2005, 925.
    • (2005) Nat Rev Microbiol , vol.3 , pp. 925
    • Weissman, K.J.1    Leadlay, P.F.2
  • 310
    • 60749090908 scopus 로고    scopus 로고
    • Structural basis for binding specificity between subclasses of modular polyketide synthase docking domains
    • Buchholz, T.J., Geders, T.W., Bartley, F.E., Reynolds, K.A., Smith, J.L., Sherman, D.H., Structural basis for binding specificity between subclasses of modular polyketide synthase docking domains. ACS Chem Biol 4 (2009), 41–52.
    • (2009) ACS Chem Biol , vol.4 , pp. 41-52
    • Buchholz, T.J.1    Geders, T.W.2    Bartley, F.E.3    Reynolds, K.A.4    Smith, J.L.5    Sherman, D.H.6
  • 311
    • 44049083124 scopus 로고    scopus 로고
    • Protein–protein interactions in multienzyme megasynthetases
    • Weissman, K.J., Müller, R., Protein–protein interactions in multienzyme megasynthetases. Chembiochem 9 (2008), 826–848.
    • (2008) Chembiochem , vol.9 , pp. 826-848
    • Weissman, K.J.1    Müller, R.2
  • 313
    • 84886305565 scopus 로고    scopus 로고
    • Subcellular localization of the pyoverdine biogenesis machinery of Pseudomonas aeruginosa: a membrane-associated “siderosome”
    • Imperi, F., Visca, P., Subcellular localization of the pyoverdine biogenesis machinery of Pseudomonas aeruginosa: a membrane-associated “siderosome”. FEBS (Fed Eur Biochem Soc) Lett 587 (2013), 3387–3391.
    • (2013) FEBS (Fed Eur Biochem Soc) Lett , vol.587 , pp. 3387-3391
    • Imperi, F.1    Visca, P.2
  • 314
    • 84859780045 scopus 로고    scopus 로고
    • Spatial organization of enzymes for metabolic engineering
    • Lee, H., DeLoache, W.C., Dueber, J.E., Spatial organization of enzymes for metabolic engineering. Metab Eng 14 (2012), 242–251.
    • (2012) Metab Eng , vol.14 , pp. 242-251
    • Lee, H.1    DeLoache, W.C.2    Dueber, J.E.3
  • 315
    • 85042191932 scopus 로고    scopus 로고
    • Construction of an organelle-like nanodevice via supramolecular self-assembly for robust biocatalysts
    • Li, H., Zheng, G., Zhu, S., Construction of an organelle-like nanodevice via supramolecular self-assembly for robust biocatalysts. Microb Cell Factories, 17, 2018, 26.
    • (2018) Microb Cell Factories , vol.17 , pp. 26
    • Li, H.1    Zheng, G.2    Zhu, S.3
  • 317
    • 84906248340 scopus 로고    scopus 로고
    • In vivo co-localization of enzymes on RNA scaffolds increases metabolic production in a geometrically dependent manner
    • Enzymes fused with RNA binding domains were brought together via RNA scaffolds in vivo, resulting in the increased production of pentadecane and succinate.
    • Li H, Zheng G, Zhu S: Construction of an organelle-like nanodevice via supramolecular self-assembly for robust biocatalysts. Microbial Cell Factories 2018, 17:26.
    • (2014) Nucleic Acids Res , vol.42 , pp. 9493-9503
    • Sachdeva, G.1    Garg, A.2    Godding, D.3    Way, J.C.4    Silver, P.A.5
  • 319
    • 79957458151 scopus 로고    scopus 로고
    • Chapter nineteen – metabolic pathway flux enhancement by synthetic protein scaffolding
    • C. Voigt Academic Press
    • Whitaker, W.R., Dueber, J.E., Chapter nineteen – metabolic pathway flux enhancement by synthetic protein scaffolding. Voigt, C., (eds.) Methods in enzymology, 2011, Academic Press, 447–468.
    • (2011) Methods in enzymology , pp. 447-468
    • Whitaker, W.R.1    Dueber, J.E.2
  • 320
    • 85006421915 scopus 로고    scopus 로고
    • Synthetic lipid-containing scaffolds enhance production by colocalizing enzymes
    • Myhrvold, C., Polka, J.K., Silver, P.A., Synthetic lipid-containing scaffolds enhance production by colocalizing enzymes. ACS Synth Biol 5 (2016), 1396–1403.
    • (2016) ACS Synth Biol , vol.5 , pp. 1396-1403
    • Myhrvold, C.1    Polka, J.K.2    Silver, P.A.3
  • 321
    • 77950863739 scopus 로고    scopus 로고
    • Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli
    • Moon, T.S., Dueber, J.E., Shiue, E., Prather, K.L.J., Use of modular, synthetic scaffolds for improved production of glucaric acid in engineered E. coli. Metab Eng 12 (2010), 298–305.
    • (2010) Metab Eng , vol.12 , pp. 298-305
    • Moon, T.S.1    Dueber, J.E.2    Shiue, E.3    Prather, K.L.J.4
  • 322
    • 84877256074 scopus 로고    scopus 로고
    • Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols
    • Avalos, J.L., Fink, G.R., Stephanopoulos, G., Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols. Nat Biotechnol, 31, 2013, 335.
    • (2013) Nat Biotechnol , vol.31 , pp. 335
    • Avalos, J.L.1    Fink, G.R.2    Stephanopoulos, G.3
  • 323
    • 84867581908 scopus 로고    scopus 로고
    • Designing synthetic regulatory networks capable of self-organizing cell polarization
    • Chau Angela, H., Walter Jessica, M., Gerardin, J., Tang, C., Lim Wendell, A., Designing synthetic regulatory networks capable of self-organizing cell polarization. Cell 151 (2012), 320–332.
    • (2012) Cell , vol.151 , pp. 320-332
    • Chau Angela, H.1    Walter Jessica, M.2    Gerardin, J.3    Tang, C.4    Lim Wendell, A.5
  • 324
    • 85064109825 scopus 로고    scopus 로고
    • Designer membraneless organelles enable codon reassignment of selected mRNAs in eukaryotes
    • eaaw2644
    • Reinkemeier, C.D., Girona, G.E., Lemke, E.A., Designer membraneless organelles enable codon reassignment of selected mRNAs in eukaryotes. Science, 363, 2019 eaaw2644.
    • (2019) Science , vol.363
    • Reinkemeier, C.D.1    Girona, G.E.2    Lemke, E.A.3
  • 327
    • 85020119719 scopus 로고    scopus 로고
    • A systems-level model reveals that 1,2-Propanediol utilization microcompartments enhance pathway flux through intermediate sequestration
    • Jakobson, C.M., Tullman-Ercek, D., Slininger, M.F., Mangan, N.M., A systems-level model reveals that 1,2-Propanediol utilization microcompartments enhance pathway flux through intermediate sequestration. PLoS Comput Biol, 13, 2017, e1005525.
    • (2017) PLoS Comput Biol , vol.13 , pp. e1005525
    • Jakobson, C.M.1    Tullman-Ercek, D.2    Slininger, M.F.3    Mangan, N.M.4
  • 328
    • 85018819393 scopus 로고    scopus 로고
    • De novo design of signal sequences to localize cargo to the 1,2-propanediol utilization microcompartment
    • Jakobson, C.M., Slininger Lee, M.F., Tullman-Ercek, D., De novo design of signal sequences to localize cargo to the 1,2-propanediol utilization microcompartment. Protein Sci 26 (2017), 1086–1092.
    • (2017) Protein Sci , vol.26 , pp. 1086-1092
    • Jakobson, C.M.1    Slininger Lee, M.F.2    Tullman-Ercek, D.3
  • 330
    • 84961244390 scopus 로고    scopus 로고
    • Employing bacterial microcompartment technology to engineer a shell-free enzyme-aggregate for enhanced 1,2-propanediol production in Escherichia coli
    • Lee, M.J., Brown, I.R., Juodeikis, R., Frank, S., Warren, M.J., Employing bacterial microcompartment technology to engineer a shell-free enzyme-aggregate for enhanced 1,2-propanediol production in Escherichia coli. Metab Eng 36 (2016), 48–56.
    • (2016) Metab Eng , vol.36 , pp. 48-56
    • Lee, M.J.1    Brown, I.R.2    Juodeikis, R.3    Frank, S.4    Warren, M.J.5
  • 331
    • 84964403647 scopus 로고    scopus 로고
    • Engineering formation of multiple recombinant Eut protein nanocompartments in E. coli
    • Held, M., Kolb, A., Perdue, S., Hsu, S.-Y., Bloch, S.E., Quin, M.B., Schmidt-Dannert, C., Engineering formation of multiple recombinant Eut protein nanocompartments in E. coli. Sci Rep, 6, 2016, 24359.
    • (2016) Sci Rep , vol.6 , pp. 24359
    • Held, M.1    Kolb, A.2    Perdue, S.3    Hsu, S.-Y.4    Bloch, S.E.5    Quin, M.B.6    Schmidt-Dannert, C.7
  • 332
    • 84969164978 scopus 로고    scopus 로고
    • Bacterial microcompartments: biomaterials for synthetic biology-based compartmentalization strategies
    • Chessher, A., Breitling, R., Takano, E., Bacterial microcompartments: biomaterials for synthetic biology-based compartmentalization strategies. ACS Biomater Sci Eng 1 (2015), 345–351.
    • (2015) ACS Biomater Sci Eng , vol.1 , pp. 345-351
    • Chessher, A.1    Breitling, R.2    Takano, E.3
  • 333
    • 84880953448 scopus 로고    scopus 로고
    • Engineering nanoscale protein compartments for synthetic organelles
    • Kim, E.Y., Tullman-Ercek, D., Engineering nanoscale protein compartments for synthetic organelles. Curr Opin Biotechnol 24 (2013), 627–632.
    • (2013) Curr Opin Biotechnol , vol.24 , pp. 627-632
    • Kim, E.Y.1    Tullman-Ercek, D.2
  • 336
    • 85044921427 scopus 로고    scopus 로고
    • Prokaryotic nanocompartments form synthetic organelles in a eukaryote
    • Self-assembled encapsulin are used to encapsulate proteins to prevent proteins from protelyotic degration, co-localize enzymes, and protect unstable or toxic enzymatic intermediates.
    • Glasgow JE, Asensio MA, Jakobson CM, Francis MB, Tullman-Ercek D: Influence of Electrostatics on Small Molecule Flux through a Protein Nanoreactor. ACS Synthetic Biology 2015, 4:1011-1019.
    • (2018) Nat Commun , vol.9 , pp. 1311
    • Lau, Y.H.1    Giessen, T.W.2    Altenburg, W.J.3    Silver, P.A.4
  • 337
    • 85014128145 scopus 로고    scopus 로고
    • Optimal compartmentalization strategies for metabolic microcompartments
    • Hinzpeter, F., Gerland, U., Tostevin, F., Optimal compartmentalization strategies for metabolic microcompartments. Biophys J 112 (2017), 767–779.
    • (2017) Biophys J , vol.112 , pp. 767-779
    • Hinzpeter, F.1    Gerland, U.2    Tostevin, F.3
  • 338
    • 85047876692 scopus 로고    scopus 로고
    • Spatially organizing biochemistry: choosing a strategy to translate synthetic biology to the factory
    • Jakobson, C.M., Tullman-Ercek, D., Mangan, N.M., Spatially organizing biochemistry: choosing a strategy to translate synthetic biology to the factory. Sci Rep, 8, 2018, 8196.
    • (2018) Sci Rep , vol.8 , pp. 8196
    • Jakobson, C.M.1    Tullman-Ercek, D.2    Mangan, N.M.3
  • 340
    • 84941588166 scopus 로고    scopus 로고
    • Syntheses and biological evaluation of costunolide, parthenolide, and their fluorinated analogues
    • Yang, Z.-J., Ge, W.-Z., Li, Q.-Y., Lu, Y., Gong, J.-M., Kuang, B.-J., Xi, X., Wu, H., Zhang, Q., Chen, Y., Syntheses and biological evaluation of costunolide, parthenolide, and their fluorinated analogues. J Med Chem 58 (2015), 7007–7020.
    • (2015) J Med Chem , vol.58 , pp. 7007-7020
    • Yang, Z.-J.1    Ge, W.-Z.2    Li, Q.-Y.3    Lu, Y.4    Gong, J.-M.5    Kuang, B.-J.6    Xi, X.7    Wu, H.8    Zhang, Q.9    Chen, Y.10
  • 341
    • 0142027026 scopus 로고    scopus 로고
    • Metabolic engineering for the microbial production of 1,3-propanediol
    • Nakamura, C.E., Whited, G.M., Metabolic engineering for the microbial production of 1,3-propanediol. Curr Opin Biotechnol 14 (2003), 454–459.
    • (2003) Curr Opin Biotechnol , vol.14 , pp. 454-459
    • Nakamura, C.E.1    Whited, G.M.2
  • 342
    • 84899051891 scopus 로고    scopus 로고
    • Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development
    • Paddon, C.J., Keasling, J.D., Semi-synthetic artemisinin: a model for the use of synthetic biology in pharmaceutical development. Nat Rev Microbiol, 12, 2014, 355.
    • (2014) Nat Rev Microbiol , vol.12 , pp. 355
    • Paddon, C.J.1    Keasling, J.D.2
  • 343
    • 84878848636 scopus 로고    scopus 로고
    • Advanced biofuel production by the yeast Saccharomyces cerevisiae
    • Buijs, N.A., Siewers, V., Nielsen, J., Advanced biofuel production by the yeast Saccharomyces cerevisiae. Curr Opin Chem Biol 17 (2013), 480–488.
    • (2013) Curr Opin Chem Biol , vol.17 , pp. 480-488
    • Buijs, N.A.1    Siewers, V.2    Nielsen, J.3
  • 345
    • 85040927382 scopus 로고    scopus 로고
    • Database resources of the national center for biotechnology information
    • Coordinators, N.R., Database resources of the national center for biotechnology information. Nucleic Acids Res 46 (2017), D8–D13.
    • (2017) Nucleic Acids Res , vol.46 , pp. D8-D13
    • Coordinators, N.R.1
  • 346
  • 347
    • 85067211139 scopus 로고    scopus 로고
    • Synthetic Reaction Updates.
    • Synthetic Reaction Updates. http://pubs.rsc.org/lus/synthetic-reaction-updates.
  • 348
    • 85067204108 scopus 로고    scopus 로고
    • web
    • web https://www.spresi.com/.
  • 349
    • 85059534194 scopus 로고    scopus 로고
    • A reaction transform language
    • Daylight Chemical Information Systems, Inc.
    • SMIRKS. A reaction transform language. 2007, Daylight Chemical Information Systems, Inc. http://www.daylight.com/dayhtml/doc/theory/theory.smirks.html.
    • (2007)
  • 350
    • 75549089640 scopus 로고    scopus 로고
    • The University of Minnesota Biocatalysis/Biodegradation Database: improving public access
    • Gao, J., Wackett, L.P., Ellis, L.B.M., The University of Minnesota Biocatalysis/Biodegradation Database: improving public access. Nucleic Acids Res 38 (2009), D488–D491.
    • (2009) Nucleic Acids Res , vol.38 , pp. D488-D491
    • Gao, J.1    Wackett, L.P.2    Ellis, L.B.M.3
  • 351
    • 84855499408 scopus 로고    scopus 로고
    • MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases
    • Kumar, A., Suthers, P.F., Maranas, C.D., MetRxn: a knowledgebase of metabolites and reactions spanning metabolic models and databases. BMC Bioinf, 13, 2012, 6.
    • (2012) BMC Bioinf , vol.13 , pp. 6
    • Kumar, A.1    Suthers, P.F.2    Maranas, C.D.3
  • 352
    • 84976865354 scopus 로고    scopus 로고
    • MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks
    • Moretti, S., Martin, O., Van Du, T., Bridge, A., Morgat, A., Pagni, M., MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks. Nucleic Acids Res 44 (2016), D523–D526.
    • (2016) Nucleic Acids Res , vol.44 , pp. D523-D526
    • Moretti, S.1    Martin, O.2    Van Du, T.3    Bridge, A.4    Morgat, A.5    Pagni, M.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.