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Justin Siegel

Title(s)Associate Professor, Biochemistry and Molecular Medicine
SchoolUniversity of California, Davis
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. 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. 2019 Dec 31; 4(27):22356-22362. PMID: 31909318.
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    2. 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. Nat Chem Biol. 2019 Nov 25. PMID: 31768035.
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    3. Sharmah A, Kraus M, Cutler SR, Siegel JB, Brady SM, Guo T. Toward Development of Fluorescence-Quenching-Based Biosensors for Drought Stress in Plants. Anal Chem. 2019 Dec 17; 91(24):15644-15651. PMID: 31698903.
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    4. 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. 2019; 14(4):e0214126. PMID: 30947258.
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    5. Guggenheim KG, Crawford LM, Paradisi F, Wang SC, Siegel JB. ß-Glucosidase Discovery and Design for the Degradation of Oleuropein. ACS Omega. 2018 Nov 30; 3(11):15754-15762. PMID: 30556012.
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    6. 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. J Am Chem Soc. 2018 10 17; 140(41):13260-13271. PMID: 30208271.
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    7. Su M, Guggenheim KG, Lien J, Siegel JB, Guo T. X-ray-Mediated Release of Molecules and Engineered Proteins from Nanostructure Surfaces. ACS Appl Mater Interfaces. 2018 Sep 26; 10(38):31860-31864. PMID: 30212177.
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    8. Cooper S, Sterling ALR, Kleffner R, Silversmith WM, Siegel JB. Repurposing Citizen Science Games as Software Tools for Professional Scientists. FDG. 2018 Aug; 2018. PMID: 30465045.
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    9. 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 Catal. 2018 Apr 06; 8(4):3133-3137. PMID: 29713562.
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    10. 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 Catal. 2018 Apr 06; 8(4):3322-3330. PMID: 30034923.
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    11. Clomburg JM, Contreras SC, Chou A, Siegel JB, Gonzalez R. Combination of type II fatty acid biosynthesis enzymes and thiolases supports a functional ß-oxidation reversal. Metab Eng. 2018 01; 45:11-19. PMID: 29146470.
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    12. 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. 2017 Sep 01; 33(17):2765-2767. PMID: 28481970.
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    13. 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 Chem Biol. 2017 09 15; 12(9):2465-2473. PMID: 28820936.
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    14. 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 Thermoplasma volcanium. ACS Omega. 2017 Jul 31; 2(7):3308-3314. PMID: 31457655.
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    15. 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. 2017; 12(5):e0176255. PMID: 28531185.
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    16. Soh LMJ, 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 Synth Biol. 2017 04 21; 6(4):610-618. PMID: 28052191.
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    17. 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. 2016 11; 12(11):2054-2068. PMID: 27540766.
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    18. 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. Nat Commun. 2016 06 07; 7:11912. PMID: 27271283.
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    19. O'Brien TE, Bertolani SJ, Tantillo DJ, Siegel JB. Mechanistically informed predictions of binding modes for carbocation intermediates of a sesquiterpene synthase reaction. Chem Sci. 2016 Jul 01; 7(7):4009-4015. PMID: 30155043.
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    20. Lucas JE, Siegel JB. Erratum: Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase. Protein Sci. 2016 Mar; 25(3):769-70. PMID: 26898461.
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    21. 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. Kinetic Characterization of 100 Glycoside Hydrolase Mutants Enables the Discovery of Structural Features Correlated with Kinetic Constants. PLoS One. 2016; 11(1):e0147596. PMID: 26815142.
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    22. Bertolani SJ, Carlin DA, Siegel JB. Computational Introduction of Catalytic Activity into Proteins. Methods Mol Biol. 2016; 1414:213-31. PMID: 27094294.
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    23. 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. Nat Commun. 2015 Nov 24; 6:10005. PMID: 26598135.
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    24. Wolf C, Siegel JB, Tinberg C, Camarca A, Gianfrani C, Paski S, Guan R, Montelione G, Baker D, Pultz IS. 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. PMID: 26374198.
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    25. Poust S, Piety J, Bar-Even A, Louw C, Baker D, Keasling JD, Siegel JB. Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction. Chembiochem. 2015 Sep 07; 16(13):1950-1954. PMID: 26109266.
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    26. Rai N, Ferreiro A, Neckelmann A, Soon A, Yao A, Siegel J, Facciotti MT, Tagkopoulos I. RiboTALE: A modular, inducible system for accurate gene expression control. Sci Rep. 2015 May 29; 5:10658. PMID: 26023068.
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    27. Lucas JE, Siegel JB. Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase. Protein Sci. 2015 Jun; 24(6):936-45. PMID: 25752240.
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    28. 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. Computational protein design enables a novel one-carbon assimilation pathway. Proc Natl Acad Sci U S A. 2015 Mar 24; 112(12):3704-9. PMID: 25775555.
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    29. Carlin DA, Bertolani SJ, Siegel JB. Biocatalytic conversion of ethylene to ethylene oxide using an engineered toluene monooxygenase. Chem Commun (Camb). 2015 Feb 11; 51(12):2283-5. PMID: 25558486.
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    30. Mak WS, Siegel JB. Computational enzyme design: transitioning from catalytic proteins to enzymes. Curr Opin Struct Biol. 2014 Aug; 27:87-94. PMID: 25005925.
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    31. 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. Proc Natl Acad Sci U S A. 2014 Jun 03; 111(22):8013-8. PMID: 24847076.
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    32. 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. J Mol Biol. 2013 Apr 26; 425(8):1378-89. PMID: 23396064.
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    33. Gordon SR, Stanley EJ, Wolf S, Toland A, Wu SJ, Hadidi D, Mills JH, Baker D, Pultz IS, Siegel JB. Computational design of an a-gliadin peptidase. J Am Chem Soc. 2012 Dec 19; 134(50):20513-20. PMID: 23153249.
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    34. 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 Synth Biol. 2013 Jan 18; 2(1):59-62. PMID: 23656326.
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    35. 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. Nat Biotechnol. 2012 Jan 22; 30(2):190-2. PMID: 22267011.
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    36. 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. Improvement of a potential anthrax therapeutic by computational protein design. J Biol Chem. 2011 Sep 16; 286(37):32586-92. PMID: 21768086.
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    37. 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. 2010 Jul 16; 329(5989):309-13. PMID: 20647463.
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