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Justin Siegel, PhD

Title(s)Associate Professor, Biochemistry and Molecular Medicine
SchoolUniversity of California, Davis
Address451 Health Sciences Drive
CA 95616
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    1. Macromolecular modeling and design in Rosetta: recent methods and frameworks. Nat Methods. 2020 Jun 01. 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, Bradley P, Bystroff C, Conway P, Cooper S, Correia BE, Coventry B, Das R, De Jong RM, DiMaio F, Dsilva L, Dunbrack R, Ford AS, Frenz B, Fu DY, Geniesse C, Goldschmidt L, Gowthaman R, Gray JJ, Gront D, Guffy S, Horowitz S, Huang PS, Huber T, Jacobs TM, Jeliazkov JR, Johnson DK, Kappel K, Karanicolas J, Khakzad H, Khar KR, Khare SD, Khatib F, Khramushin A, King IC, Kleffner R, Koepnick B, Kortemme T, Kuenze G, Kuhlman B, Kuroda D, Labonte JW, Lai JK, Lapidoth G, Leaver-Fay A, Lindert S, Linsky T, London N, Lubin JH, Lyskov S, Maguire J, Malmström L, Marcos E, Marcu O, Marze NA, Meiler J, Moretti R, Mulligan VK, Nerli S, Norn C, Ó'Conchúir S, Ollikainen N, Ovchinnikov S, Pacella MS, Pan X, Park H, Pavlovicz RE, Pethe M, Pierce BG, Pilla KB, Raveh B, Renfrew PD, Burman SSR, Rubenstein A, Sauer MF, Scheck A, Schief W, Schueler-Furman O, Sedan Y, Sevy AM, Sgourakis NG, Shi L, Siegel JB, Silva DA, Smith S, Song Y, Stein A, Szegedy M, Teets FD, Thyme SB, Wang RY, Watkins A, Zimmerman L, Bonneau R. PMID: 32483333.
      View in: PubMed   Mentions:    Fields:    
    2. Functional characterization and reclassification of an enzyme previously proposed to be a limonoid UDP-glucosyltransferase. J Sci Food Agric. 2020 Jun 01. Cui Y, Allmon SD, Siegel JB. PMID: 32483918.
      View in: PubMed   Mentions:    Fields:    
    3. Evaluating Protein Engineering Thermostability Prediction Tools Using an Independently Generated Dataset. ACS Omega. 2020 Mar 31; 5(12):6487-6493. Huang P, Chu SKS, Frizzo HN, Connolly MP, Caster RW, Siegel JB. PMID: 32258884.
      View in: PubMed   Mentions:
    4. Development of potent inhibitors of the human microsomal epoxide hydrolase. Eur J Med Chem. 2020 May 01; 193:112206. Barnych B, Singh N, Negrel S, Zhang Y, Magis D, Roux C, Hua X, Ding Z, Morisseau C, Tantillo DJ, Siegel JB, Hammock BD. PMID: 32203787.
      View in: PubMed   Mentions:    Fields:    
    5. A Benchmark for Homomeric Enzyme Active Site Structure Prediction Highlights the Importance of Accurate Modeling of Protein Symmetry. ACS Omega. 2019 Dec 31; 4(27):22356-22362. Contreras SC, Bertolani SJ, Siegel JB. PMID: 31909318.
      View in: PubMed   Mentions:
    6. Engineering a nicotinamide mononucleotide redox cofactor system for biocatalysis. Nat Chem Biol. 2020 01; 16(1):87-94. Black WB, Zhang L, Mak WS, Maxel S, Cui Y, King E, Fong B, Sanchez Martinez A, Siegel JB, Li H. PMID: 31768035.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    7. Toward Development of Fluorescence-Quenching-Based Biosensors for Drought Stress in Plants. Anal Chem. 2019 12 17; 91(24):15644-15651. Sharmah A, Kraus M, Cutler SR, Siegel JB, Brady SM, Guo T. PMID: 31698903.
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    8. Switching on a Nontraditional Enzymatic Base—Deprotonation by Serine in the ent -Kaurene Synthase from Bradyrhizobium japonicum. ACS Catalysis. 2019 Oct 4; 9(10):8867-8871. Meirong Jia, Yue Zhang, Justin B. Siegel, Dean J. Tantillo, Reuben J. Peters. .
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    9. Molecular annotation of food – towards personalized diet and precision health. Trends in Food Science & Technology. 2019 Sep 1; 91:675-680. Junai Gan, Justin B. Siegel, J. Bruce German. .
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    10. Switching on a Nontraditional Enzymatic Base - Deprotonation by Serine in the ent-Kaurene Synthase from Bradyrhizobium japonicum. ACS Catal. 2019 Oct 04; 9(10):8867-8871. Jia M, Zhang Y, Siegel JB, Tantillo DJ, Peters RJ. PMID: 32489716.
      View in: PubMed   Mentions:
    11. Computer-Aided Drug Design for Undergraduates. Journal of Chemical Education. 2019 May 14; 96(5):920-925. Dean J. Tantillo, Justin B. Siegel, Carla M. Saunders, Teresa A. Palazzo, Phillip P. Painter, Terrence E. O’Brien, Nicole N. Nuñez, Dustin H. Nouri, Michael W. Lodewyk, Brandi M. Hudson, Stephanie R. Hare, Rebecca L. Davis. .
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    12. A new benchmark illustrates that integration of geometric constraints inferred from enzyme reaction chemistry can increase enzyme active site modeling accuracy. PLoS One. 2019; 14(4):e0214126. Bertolani SJ, Siegel JB. PMID: 30947258.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    13. ß-Glucosidase Discovery and Design for the Degradation of Oleuropein. ACS Omega. 2018 Nov 30; 3(11):15754-15762. Guggenheim KG, Crawford LM, Paradisi F, Wang SC, Siegel JB. PMID: 30556012.
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    14. The Zinc Linchpin Motif in the DNA Repair Glycosylase MUTYH: Identifying the Zn2+ Ligands and Roles in Damage Recognition and Repair. J Am Chem Soc. 2018 10 17; 140(41):13260-13271. Nuñez NN, Khuu C, Babu CS, Bertolani SJ, Rajavel AN, Spear JE, Armas JA, Wright JD, Siegel JB, Lim C, David SS. PMID: 30208271.
      View in: PubMed   Mentions: 1     Fields:    Translation:HumansAnimalsCells
    15. X-ray-Mediated Release of Molecules and Engineered Proteins from Nanostructure Surfaces. ACS Appl Mater Interfaces. 2018 Sep 26; 10(38):31860-31864. Su M, Guggenheim KG, Lien J, Siegel JB, Guo T. PMID: 30212177.
      View in: PubMed   Mentions:    Fields:    
    16. Repurposing Citizen Science Games as Software Tools for Professional Scientists. FDG. 2018 Aug; 2018. Cooper S, Sterling ALR, Kleffner R, Silversmith WM, Siegel JB. PMID: 30465045.
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    17. Predicting Productive Binding Modes for Substrates and Carbocation Intermediates in Terpene Synthases-Bornyl Diphosphate Synthase as a Representative Case. ACS Catal. 2018 Apr 06; 8(4):3322-3330. O'Brien TE, Bertolani SJ, Zhang Y, Siegel JB, Tantillo DJ. PMID: 30034923.
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    18. Changing Face: A Key Residue for the Addition of Water by Sclareol Synthase. ACS Catal. 2018 Apr 06; 8(4):3133-3137. Jia M, O'Brien TE, Zhang Y, Siegel JB, Tantillo DJ, Peters RJ. PMID: 29713562.
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    19. Combination of type II fatty acid biosynthesis enzymes and thiolases supports a functional ß-oxidation reversal. Metab Eng. 2018 01; 45:11-19. Clomburg JM, Contreras SC, Chou A, Siegel JB, Gonzalez R. PMID: 29146470.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    20. Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta. Bioinformatics. 2017 Sep 01; 33(17):2765-2767. Kleffner R, Flatten J, Leaver-Fay A, Baker D, Siegel JB, Khatib F, Cooper S. PMID: 28481970.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    21. Elucidating Substrate Promiscuity within the FabI Enzyme Family. ACS Chem Biol. 2017 09 15; 12(9):2465-2473. Freund GS, O'Brien TE, Vinson L, Carlin DA, Yao A, Mak WS, Tagkopoulos I, Facciotti MT, Tantillo DJ, Siegel JB. PMID: 28820936.
      View in: PubMed   Mentions:    Fields:    Translation:HumansAnimalsCells
    22. Systematic Functional Analysis of Active-Site Residues in l-Threonine Dehydrogenase from Thermoplasma volcanium. ACS Omega. 2017 Jul 31; 2(7):3308-3314. Desjardins M, Mak WS, O'Brien TE, Carlin DA, Tantillo DJ, Siegel JB. PMID: 31457655.
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    23. 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. 2017; 12(5):e0176255. Carlin DA, Hapig-Ward S, Chan BW, Damrau N, Riley M, Caster RW, Bethards B, Siegel JB. PMID: 28531185.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    24. Engineering a Thermostable Keto Acid Decarboxylase Using Directed Evolution and Computationally Directed Protein Design. ACS Synth Biol. 2017 04 21; 6(4):610-618. Soh LMJ, Mak WS, Lin PP, Mi L, Chen FY, Damoiseaux R, Siegel JB, Liao JC. PMID: 28052191.
      View in: PubMed   Mentions: 1     Fields:    Translation:Cells
    25. 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. 2016 11; 12(11):2054-2068. Seo E, Woo J, Park E, Bertolani SJ, Siegel JB, Choi D, Dinesh-Kumar SP. PMID: 27540766.
      View in: PubMed   Mentions: 4     Fields:    Translation:HumansAnimalsCells
    26. Corrigendum: Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nat Commun. 2016 06 07; 7:11912. Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel JB. PMID: 27271283.
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    27. Mechanistically informed predictions of binding modes for carbocation intermediates of a sesquiterpene synthase reaction. Chem Sci. 2016 Jul 01; 7(7):4009-4015. O'Brien TE, Bertolani SJ, Tantillo DJ, Siegel JB. PMID: 30155043.
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    28. Erratum: Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase. Protein Sci. 2016 Mar; 25(3):769-70. Lucas JE, Siegel JB. PMID: 26898461.
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    29. Kinetic Characterization of 100 Glycoside Hydrolase Mutants Enables the Discovery of Structural Features Correlated with Kinetic Constants. PLoS One. 2016; 11(1):e0147596. 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, Tagkopoulos I, Siegel JB. PMID: 26815142.
      View in: PubMed   Mentions: 6     Fields:    Translation:HumansCells
    30. Computational Introduction of Catalytic Activity into Proteins. Methods Mol Biol. 2016; 1414:213-31. Bertolani SJ, Carlin DA, Siegel JB. PMID: 27094294.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    31. Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nat Commun. 2015 Nov 24; 6:10005. Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel JB. PMID: 26598135.
      View in: PubMed   Mentions: 8     Fields:    Translation:Cells
    32. Engineering of Kuma030: A Gliadin Peptidase That Rapidly Degrades Immunogenic Gliadin Peptides in Gastric Conditions. J Am Chem Soc. 2015 Oct 14; 137(40):13106-13. Wolf C, Siegel JB, Tinberg C, Camarca A, Gianfrani C, Paski S, Guan R, Montelione G, Baker D, Pultz IS. PMID: 26374198.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    33. Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction. Chembiochem. 2015 Sep 07; 16(13):1950-1954. Poust S, Piety J, Bar-Even A, Louw C, Baker D, Keasling JD, Siegel JB. PMID: 26109266.
      View in: PubMed   Mentions: 1     Fields:    
    34. RiboTALE: A modular, inducible system for accurate gene expression control. Sci Rep. 2015 May 29; 5:10658. Rai N, Ferreiro A, Neckelmann A, Soon A, Yao A, Siegel J, Facciotti MT, Tagkopoulos I. PMID: 26023068.
      View in: PubMed   Mentions: 1     Fields:    
    35. Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase. Protein Sci. 2015 Jun; 24(6):936-45. Lucas JE, Siegel JB. PMID: 25752240.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    36. Reassigning the Structures of Natural Products Using NMR Chemical Shifts Computed with Quantum Mechanics: A Laboratory Exercise. Journal of Chemical Education. 2015 Mar 10; 92(3):561-566. Teresa A. Palazzo, Tiana T. Truong, Shirley M. T. Wong, Emma T. Mack, Michael W. Lodewyk, Jason G. Harrison, R. Alan Gamage, Justin B. Siegel, Mark J. Kurth, Dean J. Tantillo. .
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    37. Computational protein design enables a novel one-carbon assimilation pathway. Proc Natl Acad Sci U S A. 2015 Mar 24; 112(12):3704-9. 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, Stoddard BL, Lidstrom ME, Baker D. PMID: 25775555.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    38. Biocatalytic conversion of ethylene to ethylene oxide using an engineered toluene monooxygenase. Chem Commun (Camb). 2015 Feb 11; 51(12):2283-5. Carlin DA, Bertolani SJ, Siegel JB. PMID: 25558486.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    39. Computational enzyme design: transitioning from catalytic proteins to enzymes. Curr Opin Struct Biol. 2014 Aug; 27:87-94. Mak WS, Siegel JB. PMID: 25005925.
      View in: PubMed   Mentions: 7     Fields:    Translation:Cells
    40. Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase. Proc Natl Acad Sci U S A. 2014 Jun 03; 111(22):8013-8. Preiswerk N, Beck T, Schulz JD, Milovník P, Mayer C, Siegel JB, Baker D, Hilvert D. PMID: 24847076.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    41. Janus: prediction and ranking of mutations required for functional interconversion of enzymes. J Mol Biol. 2013 Apr 26; 425(8):1378-89. Addington TA, Mertz RW, Siegel JB, Thompson JM, Fisher AJ, Filkov V, Fleischman NM, Suen AA, Zhang C, Toney MD. PMID: 23396064.
      View in: PubMed   Mentions: 5     Fields:    Translation:Cells
    42. Computational design of an a-gliadin peptidase. J Am Chem Soc. 2012 Dec 19; 134(50):20513-20. Gordon SR, Stanley EJ, Wolf S, Toland A, Wu SJ, Hadidi D, Mills JH, Baker D, Pultz IS, Siegel JB. PMID: 23153249.
      View in: PubMed   Mentions: 13     Fields:    Translation:Cells
    43. Expanding the product profile of a microbial alkane biosynthetic pathway. ACS Synth Biol. 2013 Jan 18; 2(1):59-62. 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. PMID: 23656326.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    44. Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nat Biotechnol. 2012 Jan 22; 30(2):190-2. Eiben CB, Siegel JB, Bale JB, Cooper S, Khatib F, Shen BW, Players F, Stoddard BL, Popovic Z, Baker D. PMID: 22267011.
      View in: PubMed   Mentions: 49     Fields:    Translation:HumansCells
    45. Improvement of a potential anthrax therapeutic by computational protein design. J Biol Chem. 2011 Sep 16; 286(37):32586-92. 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, Baker D, Siegel JB. PMID: 21768086.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    46. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science. 2010 Jul 16; 329(5989):309-13. 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. PMID: 20647463.
      View in: PubMed   Mentions: 177     Fields:    Translation:Cells
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