ArticleNature communications2020
Ensemble-based enzyme design can recapitulate the effects of laboratory directed evolution in silico.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
- Predicting Activation Barriers With Ring and Bond Critical Points in the Kemp Elimination Reaction.Chemphyschem : a European journal of chemical physics and physical chemistry · 2026Article
- Multistate Enzyme Design Enables Efficient and Stereoselective Multistep Catalysis.bioRxiv : the preprint server for biology · 2026Article
- Density Functional Theory Charge Delocalization Error Determines Computed Activation Barriers in Enzymatic Kemp Elimination.Chembiochem : a European journal of chemical biology · 2026Article
- Emergence of specific binding and catalysis from a designed generalist binding protein.Nature chemistry · 2026Article
- Zero-shot design of abioRxiv : the preprint server for biology · 2026Article
- Customizing the structure of minimal TIM barrels to craft efficient de novo enzymes.Nature chemical biology · 2026Article
- From possibility to precision in macromolecular ensemble prediction.Nature methods · 2026Article
- s_mmpbsa: A Lite and Cross-Platform MM-PBSA Program.Molecules (Basel, Switzerland) · 2026Article
- Rectifying AI-generated protein structure ensembles for equilibrium using physics-based computations.bioRxiv : the preprint server for biology · 2026Article
- Structure-activity relationships in catalytic amyloids.Journal of inorganic biochemistry · 2026Article
- Conformational Dynamics and Catalytic Backups in a Hyper-thermostable Engineered Archaeal Protein Tyrosine Phosphatase.JACS Au · 2026Article
- Article
- Hydrogen-deuterium exchange reveals catalytically linked protein flexibility in myoglobin-mediated intramolecular C(spProtein science : a publication of the Protein Society · 2026Article
- Modeling protein-small molecule conformational ensembles with PLACER.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Distal mutations enhance catalysis in designed enzymes by facilitating substrate binding and product release.Nature communications · 2025Article
- Modeling protein-small molecule conformational ensembles with PLACER.bioRxiv : the preprint server for biology · 2025Article
- Enhancing Cold Adaptation of Bidomain Amylases by High-Throughput Computational Engineering.Angewandte Chemie (International ed. in English) · 2025Article
- SubTuner leverages physics-based modeling to complement AI in enzyme engineering toward non-native substrates.Chem catalysis · 2025Article
- Computational loop reconstruction based design of efficient PET hydrolases.Communications biology · 2025Article
- Computational design of serine hydrolases.Science (New York, N.Y.) · 2025Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
The creation of artificial enzymes is a key objective of computational protein design. Although de novo enzymes have been successfully designed, these exhibit low catalytic efficiencies, requiring directed evolution to improve activity. Here, we use room-temperature X-ray crystallography to study changes in the conformational ensemble during evolution of the designed Kemp eliminase HG3 (k
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Registered trials
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