• 1185 Citations
  • 13 h-Index
20102019
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Research Output 2010 2019

  • 1185 Citations
  • 13 h-Index
  • 33 Article
  • 3 Comment/debate
  • 1 Chapter
  • 1 Conference contribution
2019
Open Access
reaction chemistry
Benchmarking
enzymatic reactions
active sites
Catalytic Domain

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

Students
drug
Quantum chemistry
Pharmaceutical Preparations
Teaching

Molecular annotation of food – Towards personalized diet and precision health

Gan, J., Siegel, J. B. & German, J. B., Sep 2019, In : Trends in Food Science and Technology. 91, p. 675-680 6 p.

Research output: Contribution to journalComment/debate

Diet
Food
Health
diet
food quality

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

Terpenes
Deprotonation
Serine
Switches
Reengineering
2018
4 Citations (Scopus)

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

Diterpenes
Water
Substitution reactions
Glutamine
Switches
6 Citations (Scopus)

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

Biosynthesis
Fatty acids
Catalyst supports
Fatty Acids
Enzymes
9 Citations (Scopus)

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

Terpenes
Diphosphates
Substrates
Carbon
Stereoselectivity
2 Citations (Scopus)

Repurposing citizen science games as software tools for professional scientists

Cooper, S., Sterling, A. L. R., Kleffner, R., Silversmith, W. M. & Siegel, J., Aug 7 2018, Proceedings of the 13th International Conference on the Foundations of Digital Games, FDG 2018. Deterding, S., Khandaker, M., Risi, S., Font, J., Dahlskog, S., Salge, C. & Olsson, C. M. (eds.). Association for Computing Machinery, 39

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Protein folding
Neurons
2 Citations (Scopus)

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., 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

DNA Glycosylases
DNA Repair
Zinc
Assays
DNA
2 Citations (Scopus)

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

Nanostructures
Membrane Proteins
Nanoparticles
Proteins
X rays
1 Citation (Scopus)

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

Glucosidases
Fruits
Lye
Enzymes
Caustic soda
2017
8 Citations (Scopus)

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

Substrates
Enzymes
Acyl Carrier Protein
Synthetic Chemistry Techniques
Drug Discovery
6 Citations (Scopus)

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

Keto Acids
Carboxy-Lyases
Proteins
Acids
Alcohols
11 Citations (Scopus)

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

Video Games
Sequence Alignment
Protein Structure
Licensure
Manipulation
1 Citation (Scopus)

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

L-threonine 3-dehydrogenase
Functional analysis
Enzymes
Substrates
Catalysis
3 Citations (Scopus)

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

Glycoside Hydrolases
Enzyme activity
hydrolases
thermal stability
glycosides
2016
12 Citations (Scopus)

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

Plant Genes
Cysteine Proteases
Autophagy
Ubiquitin
Yeasts

Computational introduction of catalytic activity into proteins

Bertolani, S. J., Carlin, D. A. & Siegel, J. B., May 1 2016, Methods in Molecular Biology. Humana Press Inc., Vol. 1414. p. 213-231 19 p. (Methods in Molecular Biology; vol. 1414).

Research output: Chapter in Book/Report/Conference proceedingChapter

Proteins
Software
Ligands
Enzymes

Erratum: Integrative genomic mining for enzyme function to enable engineering of a non-natural biosynthetic pathway (Nature Communications (2015) 6 (10005) DOI: 10.1038/ncomms10005)

Mak, W. S., Tran, S., Marcheschi, R., Bertolani, S., Thompson, J., Baker, D., Liao, J. C. & Siegel, J. B., Jun 7 2016, In : Nature Communications. 7, 11912.

Research output: Contribution to journalComment/debate

Biosynthetic Pathways
enzymes
communication
engineering
Enzymes
Mannitol Dehydrogenases
Catalytic Domain
Proteins
14 Citations (Scopus)

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

Glycoside Hydrolases
hydrolases
glycosides
kinetics
mutants
25 Citations (Scopus)

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

Sesquiterpenes
Tobacco
Enzymes
Reaction intermediates
Deprotonation
2015
4 Citations (Scopus)

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

Ethylene Oxide
Toluene
Mixed Function Oxygenases
Ethylene
Oxides
110 Citations (Scopus)

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

formic acid
Carbon
Proteins
Dihydroxyacetone
Dihydroxyacetone Phosphate
26 Citations (Scopus)

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

Gliadin
Peptides
Stomach
Peptide Hydrolases
Celiac Disease
31 Citations (Scopus)

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

Biosynthetic Pathways
enzymes
engineering
Enzymes
alcohols
15 Citations (Scopus)

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

Carbon
Enzymes
Formaldehyde
Kinetics
Mass spectrometry
2 Citations (Scopus)

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

Mannitol Dehydrogenases
Molecular interactions
Catalytic Domain
Pseudomonas fluorescens
Catalysis
12 Citations (Scopus)

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

Quantum theory
Chemical shift
Biological Products
mechanic
Nuclear magnetic resonance
1 Citation (Scopus)

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

Riboswitch
Synthetic Genes
Gene Expression
Gene Regulatory Networks
Proteins
2014
26 Citations (Scopus)

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

Enzymes
Proteins
62 Citations (Scopus)

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

Enzymes
X Ray Crystallography
Cycloaddition Reaction
Mutagenesis
2013
44 Citations (Scopus)

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

Alkanes
Biosynthetic Pathways
Paraffins
Fatty acids
Fatty Acids
13 Citations (Scopus)

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

Tyrosine Transaminase
Mutation
Enzymes
Aspartate Aminotransferases
Catalysis
2012
54 Citations (Scopus)

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

Gliadin
Peptide Hydrolases
Enzymes
Glutens
Celiac Disease
158 Citations (Scopus)

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

Enzymes
Crowdsourcing
Helix-Turn-Helix Motifs
X ray crystallography
Enzyme activity
2011
6 Citations (Scopus)

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

Anthrax
Capsules
Bacillus anthracis
Hydrolysis
Proteins
2010
515 Citations (Scopus)

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

Cycloaddition Reaction
Carbon
Enzymes
Substrate Specificity
Synthetic Chemistry Techniques