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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