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Justin B. Siegel, PhD - Publications

Affiliations: 
Molecular biophysics and biochemistry University of Washington, Seattle, Seattle, WA 
 2012- Chemistry University of California, Davis, Davis, CA 
Area:
computational protein design and engineering
Website:
https://sites.google.com/site/ucdsiegellab/
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55 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Mak WS, Jones CP, McBride KE, Fritz EAP, Hirsch J, German JB, Siegel JB. Acid-active proteases to optimize dietary protein digestibility: a step towards sustainable nutrition. Frontiers in Nutrition. 11: 1291685. PMID 38389801 DOI: 10.3389/fnut.2024.1291685  0.661
2023 Taylor JE, Palur DSK, Zhang A, Gonzales JN, Arredondo A, Coulther TA, Lechner ABJ, Rodriguez EP, Fiehn O, Didzbalis J, Siegel JB, Atsumi S. Awakening the natural capability of psicose production in Escherichia coli. Npj Science of Food. 7: 54. PMID 37838768 DOI: 10.1038/s41538-023-00231-0  0.573
2023 Aspacio D, Zhang Y, Cui Y, King E, Black WB, Perea S, Luu E, Siegel JB, Li H. Shifting Redox Reaction Equilibria on Demand Using an Orthogonal Redox Cofactor. Biorxiv : the Preprint Server For Biology. PMID 37693387 DOI: 10.1101/2023.08.29.555398  0.774
2023 Chan M, Siegel JB, Vater A. Design to Data for mutants of B-glucosidase B from : V311D, F248N, Y166H, Y166K, M221K. Biorxiv : the Preprint Server For Biology. PMID 37214998 DOI: 10.1101/2023.05.10.540081  0.306
2022 King E, Cui Y, Aspacio D, Nicklen F, Zhang L, Maxel S, Luo R, Siegel JB, Aitchison E, Li H. Engineering Embden-Meyerhof-Parnas Glycolysis to Generate Noncanonical Reducing Power. Acs Catalysis. 12: 8582-8592. PMID 37622090 DOI: 10.1021/acscatal.2c01837  0.795
2022 King E, Maxel S, Zhang Y, Kenney KC, Cui Y, Luu E, Siegel JB, Weiss GA, Luo R, Li H. Orthogonal glycolytic pathway enables directed evolution of noncanonical cofactor oxidase. Nature Communications. 13: 7282. PMID 36435948 DOI: 10.1038/s41467-022-35021-x  0.817
2022 Lemke C, Roach K, Ortega T, Tantillo DJ, Siegel JB, Peters RJ. Investigation of Acid-Base Catalysis in Halimadienyl Diphosphate Synthase Involved in Virulence. Acs Bio & Med Chem Au. 2: 490-498. PMID 36281298 DOI: 10.1021/acsbiomedchemau.2c00023  0.529
2022 Zhang L, King E, Black WB, Heckmann CM, Wolder A, Cui Y, Nicklen F, Siegel JB, Luo R, Paul CE, Li H. Directed evolution of phosphite dehydrogenase to cycle noncanonical redox cofactors via universal growth selection platform. Nature Communications. 13: 5021. PMID 36028482 DOI: 10.1038/s41467-022-32727-w  0.808
2022 Shu L, Gu J, Wang Q, Sun S, Cui Y, Fell J, Mak WS, Siegel JB, Shi J, Lye GJ, Baganz F, Hao J. The pyruvate decarboxylase activity of IpdC is a limitation for isobutanol production by Klebsiella pneumoniae. Biotechnology For Biofuels and Bioproducts. 15: 41. PMID 35501883 DOI: 10.1186/s13068-022-02144-8  0.776
2022 Gingrich PW, Siegel JB, Tantillo DJ. Assessing Alkene Reactivity toward Cytochrome P450-Mediated Epoxidation through Localized Descriptors and Regression Modeling. Journal of Chemical Information and Modeling. PMID 35421306 DOI: 10.1021/acs.jcim.1c01567  0.488
2021 Le KH, Adolf-Bryfogle J, Klima JC, Lyskov S, Labonte J, Bertolani S, Burman SSR, Leaver-Fay A, Weitzner B, Maguire J, Rangan R, Adrianowycz MA, Alford RF, Adal A, Nance ML, ... ... Siegel JB, et al. PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design. Biophysicist (Rockville, Md.). 2: 108-122. PMID 35128343 DOI: 10.35459/tbp.2019.000147  0.775
2021 Koehler Leman J, Lyskov S, Lewis SM, Adolf-Bryfogle J, Alford RF, Barlow K, Ben-Aharon Z, Farrell D, Fell J, Hansen WA, Harmalkar A, Jeliazkov J, Kuenze G, Krys JD, Ljubetič A, ... ... Siegel JB, et al. Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks. Nature Communications. 12: 6947. PMID 34845212 DOI: 10.1038/s41467-021-27222-7  0.768
2020 Zhang Y, Prach LM, O'Brien TE, DiMaio F, Prigozhin DM, Corn JE, Alber T, Siegel JB, Tantillo DJ. Crystal Structure and Mechanistic Molecular Modeling Studies of Diterpene Cyclase Rv3377c. Biochemistry. PMID 33182997 DOI: 10.1021/acs.biochem.0c00762  0.737
2020 Mak WS, Wang X, Arenas R, Cui Y, Bertolani SJ, Deng WQ, Tagkopoulos I, Wilson DK, Siegel JB. Discovery, Design, and Structural Characterization of Alkane Producing Enzymes across the Ferritin-like Superfamily. Biochemistry. PMID 32935984 DOI: 10.1021/Acs.Biochem.0C00665  0.8
2020 Cui Y, Allmon SD, Siegel JB. Functional characterization and reclassification of an enzyme previously proposed to be a limonoid UDP-glucosyltransferase. Journal of the Science of Food and Agriculture. PMID 32483918 DOI: 10.1002/Jsfa.10547  0.777
2020 Leman JK, Weitzner BD, Lewis SM, Adolf-Bryfogle J, Alam N, Alford RF, Aprahamian M, Baker D, Barlow KA, Barth P, Basanta B, Bender BJ, Blacklock K, Bonet J, Boyken SE, ... ... Siegel JB, et al. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nature Methods. PMID 32483333 DOI: 10.1038/S41592-020-0848-2  0.704
2020 Barnych B, Singh N, Negrel S, Zhang Y, Magis D, Roux C, Hua X, Ding Z, Morisseau C, Tantillo DJ, Siegel JB, Hammock BD. Development of potent inhibitors of the human microsomal epoxide hydrolase. European Journal of Medicinal Chemistry. 193: 112206. PMID 32203787 DOI: 10.1096/Fasebj.2020.34.S1.03639  0.54
2020 Shoemaker SR, Zhang Y, O'Brien T, Tantillo D, Siegel JB. Hybrid Quantum Mechanics/Rosetta Modeling Mechanistic Study of a Terpene Synthase Biophysical Journal. 118: 304a. DOI: 10.1016/J.Bpj.2019.11.1719  0.669
2019 Jia M, Zhang Y, Siegel JB, Tantillo DJ, Peters RJ. Switching on a Nontraditional Enzymatic Base - Deprotonation by Serine in the -Kaurene Synthase from . Acs Catalysis. 9: 8867-8871. PMID 32489716 DOI: 10.1021/Acscatal.9B02783  0.564
2019 Contreras SC, Bertolani SJ, Siegel JB. A Benchmark for Homomeric Enzyme Active Site Structure Prediction Highlights the Importance of Accurate Modeling of Protein Symmetry. Acs Omega. 4: 22356-22362. PMID 31909318 DOI: 10.1021/acsomega.9b02636  0.821
2019 Black WB, Zhang L, Mak WS, Maxel S, Cui Y, King E, Fong B, Sanchez Martinez A, Siegel JB, Li H. Engineering a nicotinamide mononucleotide redox cofactor system for biocatalysis. Nature Chemical Biology. PMID 31768035 DOI: 10.1038/S41589-019-0402-7  0.801
2019 Bertolani SJ, Siegel JB. A new benchmark illustrates that integration of geometric constraints inferred from enzyme reaction chemistry can increase enzyme active site modeling accuracy. Plos One. 14: e0214126. PMID 30947258 DOI: 10.1371/Journal.Pone.0214126  0.834
2019 Tantillo DJ, Siegel JB, Saunders CM, Palazzo TA, Painter PP, O’Brien TE, Nuñez NN, Nouri DH, Lodewyk MW, Hudson BM, Hare SR, Davis RL. Computer-Aided Drug Design for Undergraduates Journal of Chemical Education. 96: 920-925. DOI: 10.1021/Acs.Jchemed.8B00712  0.472
2018 Guggenheim KG, Crawford LM, Paradisi F, Wang SC, Siegel JB. β-Glucosidase Discovery and Design for the Degradation of Oleuropein. Acs Omega. 3: 15754-15762. PMID 30556012 DOI: 10.1021/acsomega.8b02169  0.31
2018 Nuñez NN, Khuu C, Babu CS, Bertolani SJ, Rajavel AN, Spear JE, Armas JA, Wright JD, Siegel JB, Lim C, David SS. The Zinc Linchpin Motif in the DNA Repair Glycosylase MUTYH: Identifying the Zn2+ Ligands and Roles in Damage Recognition and Repair. Journal of the American Chemical Society. PMID 30208271 DOI: 10.1021/Jacs.8B06923  0.776
2018 O'Brien TE, Bertolani SJ, Zhang Y, Siegel JB, Tantillo DJ. Predicting Productive Binding Modes for Substrates and Carbocation Intermediates in Terpene Synthases-Bornyl Diphosphate Synthase as a Representative Case. Acs Catalysis. 8: 3322-3330. PMID 30034923 DOI: 10.1021/Acscatal.8B00342  0.791
2018 Jia M, O'Brien TE, Zhang Y, Siegel JB, Tantillo DJ, Peters RJ. Changing Face: A Key Residue for the Addition of Water by Sclareol Synthase. Acs Catalysis. 8: 3133-3137. PMID 29713562 DOI: 10.1021/Acscatal.8B00121  0.687
2017 Desjardins M, Mak WS, O'Brien TE, Carlin DA, Tantillo DJ, Siegel JB. Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from . Acs Omega. 2: 3308-3314. PMID 31457655 DOI: 10.1021/acsomega.7b00519  0.801
2017 Clomburg JM, Contreras SC, Chou A, Siegel JB, Gonzalez R. Combination of type II fatty acid biosynthesis enzymes and thiolases supports a functional β-oxidation reversal. Metabolic Engineering. PMID 29146470 DOI: 10.1016/J.Ymben.2017.11.003  0.419
2017 Freund GS, O'Brien TE, Vinson L, Carlin DA, Yao A, Mak WS, Tagkopoulos I, Facciotti MT, Tantillo DJ, Siegel JB. Elucidating Substrate Promiscuity within the FabI Enzyme Family. Acs Chemical Biology. PMID 28820936 DOI: 10.1021/Acschembio.7B00400  0.798
2017 Carlin DA, Hapig-Ward S, Chan BW, Damrau N, Riley M, Caster RW, Bethards B, Siegel JB. Thermal stability and kinetic constants for 129 variants of a family 1 glycoside hydrolase reveal that enzyme activity and stability can be separately designed. Plos One. 12: e0176255. PMID 28531185 DOI: 10.1371/Journal.Pone.0176255  0.797
2017 Kleffner R, Flatten J, Leaver-Fay A, Baker D, Siegel JB, Khatib F, Cooper S. Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta. Bioinformatics (Oxford, England). PMID 28481970 DOI: 10.1093/Bioinformatics/Btx283  0.782
2017 Soh LM, Mak WS, Lin PP, Mi L, Chen FY, Damoiseaux R, Siegel JB, Liao JC. Engineering a thermostable keto acid decarboxylase using directed evolution and computationally directed protein design. Acs Synthetic Biology. PMID 28052191 DOI: 10.1021/Acssynbio.6B00240  0.728
2016 O'Brien TE, Bertolani SJ, Tantillo DJ, Siegel JB. Mechanistically informed predictions of binding modes for carbocation intermediates of a sesquiterpene synthase reaction. Chemical Science. 7: 4009-4015. PMID 30155043 DOI: 10.1039/C6Sc00635C  0.763
2016 Seo E, Woo J, Park E, Bertolani SJ, Siegel JB, Choi D, Dinesh-Kumar SP. Comparative analyses of ubiquitin-like ATG8 and cysteine protease ATG4 autophagy genes in the plant lineage and cross-kingdom processing of ATG8 by ATG4. Autophagy. 0. PMID 27540766 DOI: 10.1080/15548627.2016.1217373  0.757
2016 Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel JB. Corrigendum: Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nature Communications. 7: 11912. PMID 27271283 DOI: 10.1038/Ncomms11912  0.782
2016 Bertolani SJ, Carlin DA, Siegel JB. Computational Introduction of Catalytic Activity into Proteins. Methods in Molecular Biology (Clifton, N.J.). 1414: 213-31. PMID 27094294 DOI: 10.1007/978-1-4939-3569-7_13  0.79
2016 Lucas JE, Siegel JB. Erratum: Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase. Protein Science : a Publication of the Protein Society. 25: 769-70. PMID 26898461 DOI: 10.1002/Pro.2882  0.325
2016 Carlin DA, Caster RW, Wang X, Betzenderfer SA, Chen CX, Duong VM, Ryklansky CV, Alpekin A, Beaumont N, Kapoor H, Kim N, Mohabbot H, Pang B, Teel R, Whithaus L, ... ... Siegel JB, et al. Kinetic Characterization of 100 Glycoside Hydrolase Mutants Enables the Discovery of Structural Features Correlated with Kinetic Constants. Plos One. 11: e0147596. PMID 26815142 DOI: 10.1371/Journal.Pone.0147596  0.819
2015 Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel JB. Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nature Communications. 6: 10005. PMID 26598135 DOI: 10.1038/Ncomms10005  0.809
2015 Wolf C, Siegel JB, Tinberg C, Camarca A, Gianfrani C, Paski S, Guan R, Montelione GT, Baker D, Pultz IS. Engineering of Kuma030: a gliadin peptidase that rapidly degrades immunogenic gliadin peptides in gastric conditions. Journal of the American Chemical Society. PMID 26374198 DOI: 10.1021/Jacs.5B08325  0.403
2015 Poust S, Piety J, Bar-Even A, Baker D, Keasling J, Siegel J. Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction. Chembiochem : a European Journal of Chemical Biology. PMID 26109266 DOI: 10.1002/Cbic.201500228  0.552
2015 Siegel JB, Smith AL, Poust S, Wargacki AJ, Bar-Even A, Louw C, Shen BW, Eiben CB, Tran HM, Noor E, Gallaher JL, Bale J, Yoshikuni Y, Gelb MH, Keasling JD, et al. Computational protein design enables a novel one-carbon assimilation pathway. Proceedings of the National Academy of Sciences of the United States of America. 112: 3704-9. PMID 25775555 DOI: 10.1073/Pnas.1500545112  0.625
2015 Lucas JE, Siegel JB. Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase. Protein Science : a Publication of the Protein Society. 24: 936-45. PMID 25752240 DOI: 10.1002/Pro.2669  0.385
2015 Carlin DA, Bertolani SJ, Siegel JB. Biocatalytic conversion of ethylene to ethylene oxide using an engineered toluene monooxygenase. Chemical Communications (Cambridge, England). 51: 2283-5. PMID 25558486 DOI: 10.1039/C4Cc08802F  0.769
2015 Palazzo TA, Truong TT, Wong SMT, Mack ET, Lodewyk MW, Harrison JG, Gamage RA, Siegel JB, Kurth MJ, Tantillo DJ. Reassigning the structures of natural products using NMR chemical shifts computed with quantum mechanics: A laboratory exercise Journal of Chemical Education. 92: 561-566. DOI: 10.1021/Ed4006584  0.48
2014 Mak WS, Siegel JB. Computational enzyme design: transitioning from catalytic proteins to enzymes. Current Opinion in Structural Biology. 27: 87-94. PMID 25005925 DOI: 10.1016/J.Sbi.2014.05.010  0.776
2014 Preiswerk N, Beck T, Schulz JD, Milovník P, Mayer C, Siegel JB, Baker D, Hilvert D. Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase. Proceedings of the National Academy of Sciences of the United States of America. 111: 8013-8. PMID 24847076 DOI: 10.1073/Pnas.1401073111  0.561
2013 Harger M, Zheng L, Moon A, Ager C, An JH, Choe C, Lai YL, Mo B, Zong D, Smith MD, Egbert RG, Mills JH, Baker D, Pultz IS, Siegel JB. Expanding the product profile of a microbial alkane biosynthetic pathway. Acs Synthetic Biology. 2: 59-62. PMID 23656326 DOI: 10.1021/Sb300061X  0.704
2013 Addington TA, Mertz RW, Siegel JB, Thompson JM, Fisher AJ, Filkov V, Fleischman NM, Suen AA, Zhang C, Toney MD. Janus: prediction and ranking of mutations required for functional interconversion of enzymes. Journal of Molecular Biology. 425: 1378-89. PMID 23396064 DOI: 10.1016/J.Jmb.2013.01.034  0.603
2012 Gordon SR, Stanley EJ, Wolf S, Toland A, Wu SJ, Hadidi D, Mills JH, Baker D, Pultz IS, Siegel JB. Computational design of an α-gliadin peptidase. Journal of the American Chemical Society. 134: 20513-20. PMID 23153249 DOI: 10.1021/Ja3094795  0.764
2012 Eiben CB, Siegel JB, Bale JB, Cooper S, Khatib F, Shen BW, Players F, Stoddard BL, Popovic Z, Baker D. Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nature Biotechnology. 30: 190-2. PMID 22267011 DOI: 10.1038/Nbt.2109  0.774
2011 Wu SJ, Eiben CB, Carra JH, Huang I, Zong D, Liu P, Wu CT, Nivala J, Dunbar J, Huber T, Senft J, Schokman R, Smith MD, Mills JH, Friedlander AM, ... ... Siegel JB, et al. Improvement of a potential anthrax therapeutic by computational protein design. The Journal of Biological Chemistry. 286: 32586-92. PMID 21768086 DOI: 10.1074/Jbc.M111.251041  0.716
2011 Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, Clair JLS, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL, Houk KN, Michael FE, Baker D. A Biocatalytic Diels-Alder Reaction Using a DesignedEnzyme Synfacts. 2011: 323-323. DOI: 10.1055/S-0030-1259455  0.745
2010 Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR, St Clair JL, Gallaher JL, Hilvert D, Gelb MH, Stoddard BL, Houk KN, Michael FE, Baker D. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science (New York, N.Y.). 329: 309-13. PMID 20647463 DOI: 10.1126/Science.1190239  0.803
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