• 1328 Citations
  • 15 h-Index
20102020

Research output per year

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Research Output

  • 1328 Citations
  • 15 h-Index
  • 40 Article
  • 3 Comment/debate
  • 1 Chapter
  • 1 Conference contribution
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Article
2010

Computational design of an enzyme catalyst for a stereoselective bimolecular diels-alder reaction

Siegel, J., Zanghellini, A., Lovick, H. M., Kiss, G., Lambert, A. R., St.Clair, J. L., Gallaher, J. L., Hilvert, D., Gelb, M. H., Stoddard, B. L., Houk, K. N., Michael, F. E. & Baker, D., Jul 16 2010, In : Science. 329, 5989, p. 309-313 5 p.

Research output: Contribution to journalArticle

548 Scopus citations
2011

Improvement of a potential anthrax therapeutic by computational protein design

Wu, S. J., Eiben, C. B., Carra, J. H., Huang, I., Zong, D., Liu, P., Wu, C. T., Nivala, J., Dunbar, J., Huber, T., Senft, J., Schokman, R., Smith, M. D., Mills, J. H., Friedlander, A. M., Baker, D. & Siegel, J., Sep 16 2011, In : Journal of Biological Chemistry. 286, 37, p. 32586-32592 7 p.

Research output: Contribution to journalArticle

6 Scopus citations
2012

Computational design of an α-gliadin peptidase

Gordon, S. R., Stanley, E. J., Wolf, S., Toland, A., Wu, S. J., Hadidi, D., Mills, J. H., Baker, D., Pultz, I. S. & Siegel, J., Dec 19 2012, In : Journal of the American Chemical Society. 134, 50, p. 20513-20520 8 p.

Research output: Contribution to journalArticle

60 Scopus citations

Increased Diels-Alderase activity through backbone remodeling guided by Foldit players

Eiben, C. B., Siegel, J., Bale, J. B., Cooper, S., Khatib, F., Shen, B. W., Players, F., Stoddard, B. L., Popovic, Z. & Baker, D., Feb 2012, In : Nature Biotechnology. 30, 2, p. 190-192 3 p.

Research output: Contribution to journalArticle

165 Scopus citations
2013

Expanding the product profile of a microbial alkane biosynthetic pathway

Harger, M., Zheng, L., Moon, A., Ager, C., An, J. H., Choe, C., Lai, Y. L., Mo, B., Zong, D., Smith, M. D., Egbert, R. G., Mills, J. H., Baker, D., Pultz, I. S. & Siegel, J., Jan 18 2013, In : ACS Synthetic Biology. 2, 1, p. 59-62 4 p.

Research output: Contribution to journalArticle

47 Scopus citations

Janus: Prediction and ranking of mutations required for functional interconversion of enzymes

Addington, T. A., Mertz, R. W., Siegel, J., Thompson, J. M., Fisher, A. J., Filkov, V., Fleischman, N. M., Suen, A. A., Zhang, C. & Toney, M. D., Apr 26 2013, In : Journal of Molecular Biology. 425, 8, p. 1378-1389 12 p.

Research output: Contribution to journalArticle

14 Scopus citations
2014

Computational enzyme design: Transitioning from catalytic proteins to enzymes

Mak, W. S. & Siegel, J., 2014, In : Current Opinion in Structural Biology. 27, 1, p. 87-94 8 p.

Research output: Contribution to journalArticle

29 Scopus citations

Impact of scaffold rigidity on the design and evolution of an artificial Diels-Alderase

Preiswerk, N., Beck, T., Schulz, J. D., Milovník, P., Mayer, C., Siegel, J., Baker, D. & Hilvert, D., Jun 3 2014, In : Proceedings of the National Academy of Sciences of the United States of America. 111, 22, p. 8013-8018 6 p.

Research output: Contribution to journalArticle

68 Scopus citations
2015

Biocatalytic conversion of ethylene to ethylene oxide using an engineered toluene monooxygenase

Carlin, D. A., Bertolani, S. J. & Siegel, J., Feb 11 2015, In : Chemical Communications. 51, 12, p. 2283-2285 3 p.

Research output: Contribution to journalArticle

5 Scopus citations

Computational protein design enables a novel one-carbon assimilation pathway

Siegel, J., Smith, A. L., Poust, S., Wargacki, A. J., Bar-Even, A., Louw, C., Shen, B. W., Eiben, C. B., Tran, H. M., Noor, E., Gallaher, J. L., Bale, J., Yoshikuni, Y., Gelb, M. H., Keasling, J. D., Stoddard, B. L., Lidstrom, M. E. & Baker, D., Mar 24 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 12, p. 3704-3709 6 p.

Research output: Contribution to journalArticle

133 Scopus citations

Engineering of Kuma030: A Gliadin Peptidase That Rapidly Degrades Immunogenic Gliadin Peptides in Gastric Conditions

Wolf, C., Siegel, J., Tinberg, C., Camarca, A., Gianfrani, C., Paski, S., Guan, R., Montelione, G., Baker, D. & Pultz, I. S., Oct 14 2015, In : Journal of the American Chemical Society. 137, 40, p. 13106-13113 8 p.

Research output: Contribution to journalArticle

34 Scopus citations

Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway

Mak, W. S., Tran, S., Marcheschi, R., Bertolani, S., Thompson, J., Baker, D., Liao, J. C. & Siegel, J., Nov 24 2015, In : Nature Communications. 6, 10005.

Research output: Contribution to journalArticle

38 Scopus citations

Mechanistic Analysis of an Engineered Enzyme that Catalyzes the Formose Reaction

Poust, S., Piety, J., Bar-Even, A., Louw, C., Baker, D., Keasling, J. D. & Siegel, J., Sep 1 2015, In : ChemBioChem. 16, 13, p. 1950-1954 5 p.

Research output: Contribution to journalArticle

16 Scopus citations

Quantitative functional characterization of conserved molecular interactions in the active site of mannitol 2-dehydrogenase

Lucas, J. E. & Siegel, J., Jun 1 2015, In : Protein Science. 24, 6, p. 936-945 10 p.

Research output: Contribution to journalArticle

2 Scopus citations

Reassigning the structures of natural products using NMR chemical shifts computed with quantum mechanics: A laboratory exercise

Palazzo, T. A., Truong, T. T., Wong, S. M. T., Mack, E. T., Lodewyk, M. W., Harrison, J. G., Gamage, R. A., Siegel, J., Kurth, M. J. & Tantillo, D. J., Mar 10 2015, In : Journal of Chemical Education. 92, 3, p. 561-566 6 p.

Research output: Contribution to journalArticle

12 Scopus citations

RiboTALE: A modular, inducible system for accurate gene expression control

Rai, N., Ferreiro, A., Neckelmann, A., Soon, A., Yao, A., Siegel, J., Facciotti, M. T. & Tagkopoulos, I., May 29 2015, In : Scientific Reports. 5, 10658.

Research output: Contribution to journalArticle

2 Scopus citations
2016

Comparative analyses of ubiquitin-like ATG8 and cysteine protease ATG4 autophagy genes in the plant lineage and cross-kingdom processing of ATG8 by ATG4

Seo, E., Woo, J., Park, E., Bertolani, S. J., Siegel, J., Choi, D. & Dinesh-Kumar, S. P., Sep 17 2016, (Accepted/In press) In : Autophagy. p. 1-15 15 p.

Research output: Contribution to journalArticle

17 Scopus citations

Kinetic characterization of 100 glycoside hydrolase mutants enables the discovery of structural features correlated with kinetic constants

Carlin, D. A., Caster, R. W., Wang, X., Betzenderfer, S. A., Chen, C. X., Duong, V. M., Ryklansky, C. V., Alpekin, A., Beaumont, N., Kapoor, H., Kim, N., Mohabbot, H., Pang, B., Teel, R., Whithaus, L., Tagkopoulos, I. & Siegel, J., Jan 1 2016, In : PLoS One. 11, 1, e0147596.

Research output: Contribution to journalArticle

16 Scopus citations

Mechanistically informed predictions of binding modes for carbocation intermediates of a sesquiterpene synthase reaction

O'Brien, T. E., Bertolani, S. J., Tantillo, D. J. & Siegel, J., 2016, In : Chemical Science. 7, 7, p. 4009-4015 7 p.

Research output: Contribution to journalArticle

30 Scopus citations
2017

Elucidating Substrate Promiscuity within the FabI Enzyme Family

Freund, G. S., O'Brien, T. E., Vinson, L., Carlin, D. A., Yao, A., Mak, W. S., Tagkopoulos, I., Facciotti, M. T., Tantillo, D. J. & Siegel, J., Sep 15 2017, In : ACS Chemical Biology. 12, 9, p. 2465-2473 9 p.

Research output: Contribution to journalArticle

8 Scopus citations

Engineering a Thermostable Keto Acid Decarboxylase Using Directed Evolution and Computationally Directed Protein Design

Soh, L. M. J., Mak, W. S., Lin, P. P., Mi, L., Chen, F. Y. H., Damoiseaux, R., Siegel, J. & Liao, J. C., Apr 21 2017, In : ACS Synthetic Biology. 6, 4, p. 610-618 9 p.

Research output: Contribution to journalArticle

8 Scopus citations

Foldit Standalone: a video game-derived protein structure manipulation interface using Rosetta

Kleffner, R., Flatten, J., Leaver-Fay, A., Baker, D., Siegel, J., Khatib, F. & Cooper, S., Sep 1 2017, In : Bioinformatics (Oxford, England). 33, 17, p. 2765-2767 3 p.

Research output: Contribution to journalArticle

17 Scopus citations

Systematic Functional Analysis of Active-Site Residues in l -Threonine Dehydrogenase from Thermoplasma volcanium

Desjardins, M., Mak, W. S., O'Brien, T. E., Carlin, D. A., Tantillo, D. J. & Siegel, J., Jul 31 2017, In : ACS Omega. 2, 7, p. 3308-3314 7 p.

Research output: Contribution to journalArticle

1 Scopus citations

Thermal stability & kinetic constants for 129 variants of a family 1 glycoside hydrolase reveal that enzyme activity & stability can be separately designed

Carlin, D. A., Hapig-Ward, S., Chan, B. W., Damrau, N., Riley, M., Caster, R. W., Bethards, B. & Siegel, J., May 1 2017, In : PLoS One. 12, 5, e0176255.

Research output: Contribution to journalArticle

4 Scopus citations
2018

Changing Face: A Key Residue for the Addition of Water by Sclareol Synthase

Jia, M., O'Brien, T. E., Zhang, Y., Siegel, J., Tantillo, D. J. & Peters, R. J., Apr 6 2018, In : ACS Catalysis. 8, 4, p. 3133-3137 5 p.

Research output: Contribution to journalArticle

4 Scopus citations

Combination of type II fatty acid biosynthesis enzymes and thiolases supports a functional β-oxidation reversal

Clomburg, J. M., Contreras, S. C., Chou, A., Siegel, J. & Gonzalez, R., Jan 1 2018, In : Metabolic Engineering. 45, p. 11-19 9 p.

Research output: Contribution to journalArticle

9 Scopus citations

Predicting Productive Binding Modes for Substrates and Carbocation Intermediates in Terpene Synthases - Bornyl Diphosphate Synthase As a Representative Case

O'Brien, T. E., Bertolani, S. J., Zhang, Y., Siegel, J. & Tantillo, D. J., Apr 6 2018, In : ACS Catalysis. 8, 4, p. 3322-3330 9 p.

Research output: Contribution to journalArticle

15 Scopus citations

The Zinc Linchpin Motif in the DNA Repair Glycosylase MUTYH: Identifying the Zn2+ Ligands and Roles in Damage Recognition and Repair

Nuñez, N. N., Khuu, C., Babu, C. S., Bertolani, S. J., Rajavel, A. N., Spear, J. E., Armas, J. A., Wright, J. D., Siegel, J. B., Lim, C. & David, S. S., Oct 17 2018, In : Journal of the American Chemical Society. 140, 41, p. 13260-13271 12 p.

Research output: Contribution to journalArticle

2 Scopus citations

X-ray-Mediated Release of Molecules and Engineered Proteins from Nanostructure Surfaces

Su, M., Guggenheim, K. G., Lien, J., Siegel, J. & Guo, T., Sep 26 2018, In : ACS Applied Materials and Interfaces. 10, 38, p. 31860-31864 5 p.

Research output: Contribution to journalArticle

2 Scopus citations

β-Glucosidase Discovery and Design for the Degradation of Oleuropein

Guggenheim, K. G., Crawford, L. M., Paradisi, F., Wang, S. C. & Siegel, J., Nov 20 2018, In : ACS Omega. 3, 11, p. 15754-15762 9 p.

Research output: Contribution to journalArticle

2 Scopus citations
2019

A Benchmark for Homomeric Enzyme Active Site Structure Prediction Highlights the Importance of Accurate Modeling of Protein Symmetry

Contreras, S. C., Bertolani, S. J. & Siegel, J. B., Dec 31 2019, In : ACS Omega. 4, 27, p. 22356-22362 7 p.

Research output: Contribution to journalArticle

Open Access
Open Access
3 Scopus citations

Computer-Aided Drug Design for Undergraduates

Tantillo, D. J., Siegel, J., Saunders, C. M., Palazzo, T. A., Painter, P. P., O'Brien, T. E., Nuniez, N. N., Nouri, D. H., Lodewyk, M. W., Hudson, B. M., Hare, S. R. & Davis, R. L., Jan 1 2019, In : Journal of Chemical Education.

Research output: Contribution to journalArticle

4 Scopus citations

Engineering a nicotinamide mononucleotide redox cofactor system for biocatalysis

Black, W. B., Zhang, L., Mak, W. S., Maxel, S., Cui, Y., King, E., Fong, B., Sanchez Martinez, A., Siegel, J. B. & Li, H., Jan 1 2019, (Accepted/In press) In : Nature Chemical Biology.

Research output: Contribution to journalArticle

Switching on a Nontraditional Enzymatic Base - Deprotonation by Serine in the ent-Kaurene Synthase from Bradyrhizobium japonicum

Jia, M., Zhang, Y., Siegel, J. B., Tantillo, D. J. & Peters, R. J., Jan 1 2019, In : ACS Catalysis. 9, 10, p. 8867-8871 5 p.

Research output: Contribution to journalArticle

2 Scopus citations

Toward Development of Fluorescence-Quenching-Based Biosensors for Drought Stress in Plants

Sharmah, A., Kraus, M., Cutler, S. R., Siegel, J. B., Brady, S. M. & Guo, T., Dec 17 2019, In : Analytical chemistry. 91, 24, p. 15644-15651 8 p.

Research output: Contribution to journalArticle

2020

Development of potent inhibitors of the human microsomal epoxide hydrolase

Barnych, B., Singh, N., Negrel, S., Zhang, Y., Magis, D., Roux, C., Hua, X., Ding, Z., Morisseau, C., Tantillo, D. J., Siegel, J. B. & Hammock, B. D., May 1 2020, In : European Journal of Medicinal Chemistry. 193, 112206.

Research output: Contribution to journalArticle

Evaluating Protein Engineering Thermostability Prediction Tools Using an Independently Generated Dataset

Huang, P., Chu, S. K. S., Frizzo, H. N., Connolly, M. P., Caster, R. W. & Siegel, J. B., Jan 1 2020, (Accepted/In press) In : ACS Omega.

Research output: Contribution to journalArticle

Open Access

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Leman, J. K., Weitzner, B. D., Lewis, S. M., Adolf-Bryfogle, J., Alam, N., Alford, R. F., Aprahamian, M., Baker, D., Barlow, K. A., Barth, P., Basanta, B., Bender, B. J., Blacklock, K., Bonet, J., Boyken, S. E., Bradley, P., Bystroff, C., Conway, P., Cooper, S., Correia, B. E. & 88 others, Coventry, B., Das, R., De Jong, R. M., DiMaio, F., Dsilva, L., Dunbrack, R., Ford, A. S., Frenz, B., Fu, D. Y., Geniesse, C., Goldschmidt, L., Gowthaman, R., Gray, J. J., Gront, D., Guffy, S., Horowitz, S., Huang, P. S., Huber, T., Jacobs, T. M., Jeliazkov, J. R., Johnson, D. K., Kappel, K., Karanicolas, J., Khakzad, H., Khar, K. R., Khare, S. D., Khatib, F., Khramushin, A., King, I. C., Kleffner, R., Koepnick, B., Kortemme, T., Kuenze, G., Kuhlman, B., Kuroda, D., Labonte, J. W., Lai, J. K., Lapidoth, G., Leaver-Fay, A., Lindert, S., Linsky, T., London, N., Lubin, J. H., Lyskov, S., Maguire, J., Malmström, L., Marcos, E., Marcu, O., Marze, N. A., Meiler, J., Moretti, R., Mulligan, V. K., Nerli, S., Norn, C., Ó’Conchúir, S., Ollikainen, N., Ovchinnikov, S., Pacella, M. S., Pan, X., Park, H., Pavlovicz, R. E., Pethe, M., Pierce, B. G., Pilla, K. B., Raveh, B., Renfrew, P. D., Burman, S. S. R., Rubenstein, A., Sauer, M. F., Scheck, A., Schief, W., Schueler-Furman, O., Sedan, Y., Sevy, A. M., Sgourakis, N. G., Shi, L., Siegel, J. B., Silva, D. A., Smith, S., Song, Y., Stein, A., Szegedy, M., Teets, F. D., Thyme, S. B., Wang, R. Y. R., Watkins, A., Zimmerman, L. & Bonneau, R., Jan 1 2020, (Accepted/In press) In : Nature Methods.

Research output: Contribution to journalArticle