Justin Siegel

TitleAsst Prof
InstitutionUniversity 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. Jia M, O'Brien TE, Zhang Y, Siegel J, 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.
      View in: PubMed
    2. Kleffner R, Flatten J, Leaver-Fay A, Baker D, Siegel J, 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.
      View in: PubMed
    3. Freund GS, O'Brien TE, Vinson L, Carlin DA, Yao A, Mak WS, Tagkopoulos I, Facciotti MT, Tantillo DJ, Siegel J. Elucidating Substrate Promiscuity within the FabI Enzyme Family. ACS Chem Biol. 2017 09 15; 12(9):2465-2473. PMID: 28820936.
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    4. Carlin DA, Hapig-Ward S, Chan BW, Damrau N, Riley M, Caster RW, Bethards B, Siegel J. 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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    5. Soh LMJ, Mak WS, Lin PP, Mi L, Chen FY, Damoiseaux R, Siegel J, 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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    6. Seo E, Woo J, Park E, Bertolani SJ, Siegel J, 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 Nov; 12(11):2054-2068. PMID: 27540766.
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    7. Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel J. Corrigendum: Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nat Commun. 2016 Jun 07; 7:11912. PMID: 27271283; PMCID: PMC4899625.
    8. Lucas JE, Siegel J. 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; PMCID: PMC4815420.
    9. 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 J. 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; PMCID: PMC4729467.
    10. Bertolani SJ, Carlin DA, Siegel J. Computational Introduction of Catalytic Activity into Proteins. Methods Mol Biol. 2016; 1414:213-31. PMID: 27094294.
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    11. Mak WS, Tran S, Marcheschi R, Bertolani S, Thompson J, Baker D, Liao JC, Siegel J. Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway. Nat Commun. 2015 Nov 24; 6:10005. PMID: 26598135.
      View in: PubMed
    12. Wolf C, Siegel J, 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; PMCID: PMC4958374.
    13. Poust S, Piety J, Bar-Even A, Louw C, Baker D, Keasling JD, Siegel J. Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction. Chembiochem. 2015 Jun 24. PMID: 26109266.
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    14. 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; PMCID: PMC4650599.
    15. Lucas JE, Siegel J. 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; PMCID: PMC4456107.
    16. Siegel J, 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; PMCID: PMC4378393.
    17. Mak WS, Siegel J. Computational enzyme design: transitioning from catalytic proteins to enzymes. Curr Opin Struct Biol. 2014 Aug; 27:87-94. PMID: 25005925.
      View in: PubMed
    18. Preiswerk N, Beck T, Schulz JD, MilovnĂ­k P, Mayer C, Siegel J, 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; PMCID: PMC4050586.
    19. Addington TA, Mertz RW, Siegel J, 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; PMCID: PMC3615137.
    20. Gordon SR, Stanley EJ, Wolf S, Toland A, Wu SJ, Hadidi D, Mills JH, Baker D, Pultz IS, Siegel J. Computational design of an a-gliadin peptidase. J Am Chem Soc. 2012 Dec 19; 134(50):20513-20. PMID: 23153249; PMCID: PMC3526107.
    21. 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 J. Expanding the product profile of a microbial alkane biosynthetic pathway. ACS Synth Biol. 2013 Jan 18; 2(1):59-62. PMID: 23656326; PMCID: PMC3818147.
    22. Eiben CB, Siegel J, 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; PMCID: PMC3566767.
    23. 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 J. Improvement of a potential anthrax therapeutic by computational protein design. J Biol Chem. 2011 Sep 16; 286(37):32586-92. PMID: 21768086; PMCID: PMC3173206.
    24. Siegel J, 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; PMCID: PMC3241958.
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