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Representative peer-reviewed scientific papers that used our academic methods to design superior enzymes, antibodies, and vaccine immunogens.

Selected peer-reviewed papers that use protein stability and expression optimization:

  1. Goldenzweig, A. et al. Automated Structure- and Sequence-Based Design of Proteins for High Bacterial Expression and Stability. Mol. Cell 2016.

  2. Campeotto, I. et al. One-Step Design of a Stable Variant of the Malaria Invasion Protein RH5 for Use as a Vaccine Immunogen. Proc. Natl. Acad. Sci. U. S. A. 2017.

  3. Sherkhanov, S. et al. Isobutanol Production Freed from Biological Limits Using Synthetic Biochemistry. Nat. Commun. 2020.

  4. Hettiaratchi, M. H. et al. Reengineering Biocatalysts: Computational Redesign of Chondroitinase ABC Improves Efficacy and Stability. Sci Adv 2020.

  5. Peleg, Y. et al. Community-Wide Experimental Evaluation of the PROSS Stability-Design Method. J. Mol. Biol. 2021.

  6. Kriegel, M. et al. A PROSS-Designed Extensively Mutated Estrogen Receptor α Variant Displays Enhanced Thermal Stability While Retaining Native Allosteric Regulation and Structure. Sci. Rep. 2021.

  7. Barber-Zucker, S. et al. Stable and Functionally Diverse Versatile Peroxidases Designed Directly from Sequences. J. Am. Chem. Soc. 2022. 

Selected peer-reviewed papers that use enzyme activity optimization:

  1. Khersonsky, O. et al. Automated Design of Efficient and Functionally Diverse Enzyme Repertoires. Mol. Cell 2018.

  2. Bengel, L. L. et al. Engineered Enzymes Enable Selective N-Alkylation of Pyrazoles with Simple Haloalkanes. Angew. Chem. Int. Ed Engl. 2021.

  3. Vos, P. D. et al. Computationally Designed Hyperactive Cas9 Enzymes.
    Nat. Commun. 2022.

  4. Barber-Zucker, S. et al. Designed High-Redox Potential Laccases Exhibit High Functional Diversity. ACS Catal. 2022.

  5. Gomez de Santos, P. et al. Repertoire of Computationally Designed Peroxygenases for Enantiodivergent C-H Oxyfunctionalization Reactions.
    J. Am. Chem. Soc. 2023.

Selected peer-reviewed papers that use protein-protein interactions optimization:


  1. Netzer, R. et al. Ultrahigh Specificity in a Network of Computationally Designed Protein-Interaction Pairs. Nat. Commun. 2018.

  2. VanDrisse, C. M. et al. Computationally Designed Pyocyanin Demethylase Acts Synergistically with Tobramycin to Kill Recalcitrant Pseudomonas Aeruginosa Biofilms. Proc. Natl. Acad. Sci. U. S. A. 2021.

Selected peer-reviewed papers that show the successful humanization of therapeutic antibodies:


  1. Tennenhouse, A. et al. Reliable energy-based antibody humanization and stabilization. Nat. Biomed. Eng. (2023)

See additional peer-reviewed papers

  1. Lipsh-Sokolik, R. et al. Combinatorial Assembly and Design of Enzymes. Science 2023.

  2. Yang, S. et al. Improving the Thermostability of Glycosyltransferase YojK by Targeting Mutagenesis for Highly Efficient Biosynthesis of Rebaudioside D. Molecular Catalysis 2023.

  3. Borgert, S. R. et al. Moonlighting Chaperone Activity of the Enzyme PqsE Contributes to RhlR-Controlled Virulence of Pseudomonas Aeruginosa.
    Nat. Commun. 2022.

  4. Lv, Y. et al. Enhancing the Thermal and Kinetic Stability of Ketol-Acid Reductoisomerase, a Central Catalyst of a Cell-Free Enzyme Cascade for the Manufacture of Platform Chemicals. Applied Biosciences 2022. 

  5. Joho, Y. et al. Ancestral Sequence Reconstruction Identifies Structural Changes Underlying the Evolution of Ideonella Sakaiensis PETase and Variants with Improved Stability and Activity. Biochemistry 2022.

  6. Whitefield, C. et al. Computational Design and Experimental Characterisation of a Stable Human Heparanase Variant. RSC Chemical Biology 2022. 

  7. Beltrán, J. et al. Rapid Biosensor Development Using Plant Hormone Receptors as Reprogrammable Scaffolds. Nat. Biotechnol. 2022.

  8. Leonard, A. C. et al. Stabilization of the SARS-CoV-2 Receptor Binding Domain by Protein Core Redesign and Deep Mutational Scanning.
    Protein Eng. Des. Sel. 2022.

  9. Allouche-Arnon, H. et al. Computationally Designed Dual-Color MRI Reporters for Noninvasive Imaging of Transgene Expression.
    Nat. Biotechnol. 2022.

  10. Dong, F. et al. Insights of Conformational Dynamics on Catalytic Activity in the Computational Stability Design of Bacillus Subtilis LipA.
    Arch. Biochem. Biophys. 2022.

  11. Listov, D. et al. Assessing and Enhancing Foldability in Designed Proteins. Protein Sci. 2022.

  12. Ospina, F. et al. Selective Biocatalytic N-Methylation of Unsaturated Heterocycles.
    Angew. Chem. Int. Ed Engl. 2022.


  13. Vongsouthi, V. et al. A Rationally and Computationally Designed Fluorescent Biosensor for D-Serine. ACS Sens 2021.

  14. Hsieh, C. L. et al. Stabilized Coronavirus Spike Stem Elicits a Broadly Protective Antibody. Cell Rep. 2021.

  15. Dietler, J. et al. A Light-Oxygen-Voltage Receptor Integrates Light and Temperature. J. Mol. Biol. 2021.

  16. Mao, G. et al. Sustainable Approach for Degradation and Detoxification of Malachite Green by an Engineered Polyphenol Oxidase at High Temperature. J. Clean. Prod. 2021.

  17. Adams, E. M. et al. Local Mutations Can Serve as a Game Changer for Global Protein Solvent Interaction. JACS Au 2021.

  18. Ben-Sasson, A. J. et al. Design of Biologically Active Binary Protein 2D Materials. Nature 2021.

  19. Wang, J. et al. Enzyme Engineering and in Vivo Testing of a Formate-Reduction Pathway. Synthetic Biology 2021.

  20. Dermouche, S. et al. Optimizing the First TPR Domain of the Human SPAG1 Protein Provides Insight into the HSP70 and HSP90 Binding Properties. Biochemistry 2021.

  21. Badri, A. et al. Complete Biosynthesis of a Sulfated Chondroitin in Escherichia Coli. Nat. Commun. 2021.

  22. Xu, J. et al. Computational Design of Highly Stable and Soluble Alcohol Dehydrogenase for NADPH Regeneration.
    Bioresources and Bioprocessing 2021.

  23. Zurek, P. J. et al. Growth Amplification in Ultrahigh-Throughput Microdroplet Screening Increases Sensitivity of Clonal Enzyme Assays and Minimizes Phenotypic Variation. Lab Chip 2021.

  24. Lajoie, M. J. et al. Designed Protein Logic to Target Cells with Precise Combinations of Surface Antigens. Science 2020.

  25. Lee, K. B. et al. Generation of Highly Selective Monoclonal Antibodies Inhibiting a Recalcitrant Protease Using Decoy Designs.
    Biotechnol. Bioeng. 2020.

  26. Rezan, G. et al. Increasing Thermal Stability and Improving Biodistribution of VEGFR2-Binding Affibody Molecules by a Combination of in Silico and Directed Evolution Approaches. Scientific Reports 2020.

  27. Valliere, M. A. et al. A Bio-Inspired Cell-Free System for Cannabinoid Production from Inexpensive Inputs. Nat. Chem. Biol. 2020.

  28. Morrison, C. S. et al. Improved Soluble Expression and Use of Recombinant Human Renalase. PLoS One 2020.

  29. Georgoulia, P. S. et al. Deciphering the Molecular Mechanism of FLT3 Resistance Mutations. FEBS J. 2020.

  30. Lambert, A. R. et al. Optimization of Protein Thermostability and Exploitation of Recognition Behavior to Engineer Altered Protein-DNA Recognition. Structure 2020.

  31. Malladi, S. K. et al. One-Step Sequence and Structure-Guided Optimization of HIV-1 Envelope gp140. Current Research in Structural Biology 2020.

  32. Tullman, J. et al. A ClpS-Based N-Terminal Amino Acid Binding Reagent with Improved Thermostability and Selectivity. Biochem. Eng. J. 2020.

  33. Klaus, M. et al. Ketosynthase Domain Constrains the Design of Polyketide Synthases. ACS Chem. Biol. 2020.

  34. Risso, V. A. et al. Enhancing a DE Novo Enzyme Activity by Computationally-Focused, Ultra-Low-Throughput Sequence Screening. Chem. Sci. 2020.

  35. Lei, Y. et al. Engineering Chromosome Region Maintenance 1 Fragments That Bind to Nuclear Export Signals. Protein Sci. 2019.

  36. Zahradník, J. et al. Flexible Regions Govern Promiscuous Binding of IL-24 to Receptors IL-20R1 and IL-22R1. FEBS J. 2019.

  37. Lee, K. B. et al. Reducing Proteolytic Liability of a MMP-14 Inhibitory Antibody by Site-saturation Mutagenesis. Protein Sci. 2019.

  38. Buldun, C. M. et al. SnoopLigase Catalyzes Peptide–Peptide Locking and Enables Solid-Phase Conjugate Isolation. J. Am. Chem. Soc. 2018.

  39. Lapidoth, G. et al. Highly Active Enzymes by Automated Combinatorial Backbone Assembly and Sequence Design. Nat. Commun. 2018.

  40. Trudeau, D. L. et al. Design and in Vitro Realization of Carbon-Conserving Photorespiration. Proc. Natl. Acad. Sci. U. S. A. 2018.

  41. Gan, J. et al. Native Mass Spectrometry of Recombinant Proteins from Crude Cell Lysates. Anal. Chem. 2017.

  42. Goldsmith, M. et al. Overcoming an Optimization Plateau in the Directed Evolution of Highly Efficient Nerve Agent Bioscavengers.
    Protein Eng. Des. Sel. 2017.

  43. Vernon, R. M. et al. Stabilization of a Nucleotide-Binding Domain of the Cystic Fibrosis Transmembrane Conductance Regulator Yields Insight into Disease-Causing Mutations. J. Biol. Chem. 2017.

  44. Brazzolotto, X. et al. Bacterial Expression of Human Butyrylcholinesterase as a Tool for Nerve Agent Bioscavengers Development. Molecules 2017.

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