ArticlePloS one2011
De novo enzyme design using Rosetta3.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 144 papers.
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Who cites it
144 citing papers in PubMed.
- Unraveling a Case Where the NAC Approach Fails─MD and QM Modeling of Regioselective cis-Stilbene Oxide Hydrolysis by Engineered Epoxide Hydrolases.Journal of chemical information and modeling · 2026Article
- Generative AI for controllable protein sequence design: A survey.npj drug discovery · 2026Review
- Deep Prior Framework: integrating functional specificity with general plausibility for targeted protein evolution.Briefings in bioinformatics · 2026Article
- Controllable Protein Design by Prefix-Tuning Protein Language Models.Journal of chemical information and modeling · 2026Article
- A Hybrid Physics-Deep Learning Framework for Combinatorial De Novo Design of Small-Molecule Binding Proteins.bioRxiv : the preprint server for biology · 2026Article
- Enhancing Enzymatic Bioconjugation Efficiency via Computer-Based Installation of a Substrate Recruitment Domain.Bioconjugate chemistry · 2026Article
- Unlocking Enzyme Discovery: Leveraging Multi-Omics, Machine Learning, and De Novo Design.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Protein design drives synthetic biology research of plant natural products.Biodesign research · 2025Review
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- Efficient protein structure generation with sparse denoising models.Nature machine intelligence · 2025Article
- Cloning, Characterization, and Computer-Aided Evolution of a Thermostable Laccase of the DUF152 Family From Klebsiella michiganensis.Proteins · 2025Article
- Article
- SubTuner leverages physics-based modeling to complement AI in enzyme engineering toward non-native substrates.Chem catalysis · 2025Article
- Transitioning enzyme catalysis towards photocatalysis.Philosophical transactions. Series A, Mathematical, physical, and engineering sciences · 2025Review
- Computational design of serine hydrolases.Science (New York, N.Y.) · 2025Article
- De Novo Design of Proteins for Autocatalytic Isopeptide Bond Formation.Journal of the American Chemical Society · 2025Article
- Advances in the biological production of sugar alcohols from biomass-derived xylose.World journal of microbiology & biotechnology · 2025Review
- Self-supervised machine learning methods for protein design improve sampling but not the identification of high-fitness variants.Science advances · 2025Article
- A Practical Guide to Computational Tools for Engineering Biocatalytic Properties.International journal of molecular sciences · 2025Review
- Strand-Swapped SH3 Domain Dimer with Superoxide Dismutase Activity.ACS central science · 2025Article
84 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The Rosetta de novo enzyme design protocol has been used to design enzyme catalysts for a variety of chemical reactions, and in principle can be applied to any arbitrary chemical reaction of interest. The process has four stages: 1) choice of a catalytic mechanism and corresponding minimal model active site, 2) identification of sites in a set of scaffold proteins where this minimal active site can be realized, 3) optimization of the identities of the surrounding residues for stabilizing interactions with the transition state and primary catalytic residues, and 4) evaluation and ranking the resulting designed sequences. Stages two through four of this process can be carried out with the Rosetta package, while stage one needs to be done externally. Here, we demonstrate how to carry out the Rosetta enzyme design protocol from start to end in detail using for illustration the triosephosphate isomerase reaction.
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Registered trials
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