Research graph
References from What deep learning can and cannot (yet) do for enzyme design. Local targets link to admitted publications; unresolved targets remain external evidence.
Computational enzyme design
10.1002/anie.201204077 · 2013 · External reference
Designing better enzymes: insights from directed evolution
10.1016/j.sbi.2020.12.015 · 2021 · External reference
De novo design of all-atom biomolecular interactions with RFdiffusion3
2025 · External reference
Atom-level enzyme active site scaffolding using RFdiffusion2
10.1038/s41592-025-02975-x · 2026 · External reference
The moderately efficient enzyme: evolutionary and physicochemical trends shaping enzyme parameters
10.1021/bi2002289 · 2011 · External reference
A proficient enzyme
10.1126/science.7809611 · 1995 · External reference
BRENDA in 2026: a Global Core Biodata Resource for functional enzyme and metabolic data within the DSMZ Digital Diversity
10.1093/nar/gkaf1113 · 2026 · External reference
Precision is essential for efficient catalysis in an evolved Kemp eliminase
10.1038/nature12623 · 2013 · External reference
Emergence of a catalytic tetrad during evolution of a highly active artificial aldolase
10.1038/nchem.2596 · 2017 · External reference
Emergence of a negative activation heat capacity during evolution of a designed enzyme
10.1021/jacs.9b02731 · 2019 · External reference
De novo design of cysteine proteases
2026 · External reference
Computational design of metalloproteases
2025 · External reference
Zero-shot design of a de novo metalloenzyme
2026 · External reference
Generative artificial intelligence for enzyme design: recent advances in models and applications
2025 · External reference
Illuminating the universe of enzyme catalysis in the era of artificial intelligence
2026 · External reference
Atomic context-conditioned protein sequence design using LigandMPNN
10.1038/s41592-025-02626-1 · 2025 · External reference
Structure-conditioned masked language models for protein sequence design generalize beyond the native sequence space
2023 · External reference
Boltz-2: towards accurate and efficient binding affinity prediction
2025 · External reference
Accurate structure prediction of biomolecular interactions with AlphaFold 3
10.1038/s41586-024-07487-w · 2024 · External reference
Chai-1: decoding the molecular interactions of life
2024 · External reference
Molecular dynamics explorations of active site structure in designed and evolved enzymes
10.1021/ar500452q · 2015 · External reference
Modeling protein–small molecule conformational ensembles with PLACER
10.1073/pnas.2427161122 · 2025 · External reference
Electric fields are a key determinant of carbapenemase activity in class A β-Lactamases
10.1021/acscatal.3c05302 · 2024 · External reference
TUPÃ: electric field analyses for molecular simulations
10.1002/jcc.26873 · 2022 · External reference
Scaffolding protein functional sites using deep-learning
10.1126/science.abn2100 · 2022 · External reference
Computational enzyme design by catalytic motif scaffolding
10.1038/s41586-025-09747-9 · 2026 · External reference
Computational design of serine hydrolases
10.1126/science.adu2454 · 2025 · External reference
Computational design of metallohydrolases
10.1038/s41586-025-09746-w · 2026 · External reference
De novo design of luciferases using deep-learning
10.1038/s41586-023-05696-3 · 2023 · External reference
De novo design of porphyrin-containing proteins as efficient and stereoselective catalysts
10.1126/science.adt7268 · 2025 · External reference
Design of heme enzymes with a tunable substrate binding pocket adjacent to an open metal coordination site
10.1021/jacs.3c02742 · 2023 · External reference
Kemp elimination catalysts by computational enzyme design
10.1038/nature06879 · 2008 · External reference
De novo computational design of retro-aldol enzymes
10.1126/science.1152692 · 2008 · External reference
Complete computational design of high-efficiency Kemp elimination enzymes
10.1038/s41586-025-09136-2 · 2025 · External reference
Emergence of specific binding and catalysis from a designed generalist binding protein
10.1038/s41557-026-02125-6 · 2026 · External reference
Customizing the structure of minimal TIM barrels to craft efficient de novo enzymes
2026 · External reference
Electric fields and enzyme catalysis
10.1146/annurev-biochem-061516-044432 · 2017 · External reference
Electrostatics as a guiding principle in understanding and designing enzymes
10.1021/acs.jctc.3c01395 · 2024 · External reference
AI.zymes: a modular platform for evolutionary enzyme design
2025 · External reference
Computational optimization of electric fields for improving catalysis of a designed Kemp eliminase
10.1021/acscatal.7b03151 · 2018 · External reference
Enhanced active-site electric field accelerates enzyme catalysis
10.1038/s41557-023-01287-x · 2023 · External reference
Distal mutations in a designed retro-aldolase alter loop dynamics to shift and accelerate the rate-limiting step
10.1021/jacs.5c05134 · 2025 · External reference
Evolution of dynamical networks enhances catalysis in a designer enzyme
10.1038/s41557-021-00763-6 · 2021 · External reference
How directed evolution reshapes the energy landscape in an enzyme to boost catalysis
10.1126/science.abd3623 · 2020 · External reference
Role of conformational dynamics in the evolution of retro-aldolase activity
10.1021/acscatal.7b02954 · 2017 · External reference
Optimization of enzyme mechanism along the evolutionary trajectory of a computationally designed (retro-)aldolase
10.1021/jacs.7b05796 · 2017 · External reference
De novo design of allosterically switchable protein assemblies
10.1038/s41586-024-07813-2 · 2024 · External reference
Predicting multiple conformations via sequence clustering and AlphaFold2
10.1038/s41586-023-06832-9 · 2024 · External reference
Deep learning-guided design of dynamic proteins
10.1126/science.adr7094 · 2025 · External reference
Multi-state protein design with DynamicMPNN
2025 · External reference
Computational remodeling of an enzyme conformational landscape for altered substrate selectivity
10.1038/s41467-023-41762-0 · 2023 · External reference
Computational design of generalist cyclopropanases with stereodivergent selectivity
10.1038/s41467-026-68327-1 · 2026 · External reference
Design of efficient artificial enzymes using crystallographically enhanced conformational sampling
10.1021/jacs.4c00677 · 2024 · External reference
Scalable emulation of protein equilibrium ensembles with generative deep-learning
10.1126/science.adv9817 · 2025 · External reference
Learning millisecond protein dynamics from what is missing in NMR spectra
10.1038/s41586-026-10989-4 · 2026 · External reference
Entropy and enzyme catalysis
10.1021/acs.accounts.6b00321 · 2017 · External reference
Solvent entropy contributions to catalytic activity in designed and optimized Kemp eliminases
10.1021/acs.jpcb.7b07526 · 2018 · External reference
Investigating whether deep-learning models for co-folding learn the physics of protein-ligand interactions
10.1038/s41467-025-63947-5 · 2025 · External reference
Computational tools for the evaluation of laboratory-engineered biocatalysts
10.1039/c6cc06055b · 2017 · External reference
Simulating enzyme catalysis with electrostatically embedded machine learning potentials
10.1039/d6sc01156j · 2026 · External reference
A geometric foundation model for enzyme retrieval with evolutionary insights
10.1038/s41929-026-01478-y · 2026 · External reference
CatPred: a comprehensive framework for deep-learning in vitro enzyme kinetic parameters
10.1038/s41467-025-57215-9 · 2025 · External reference
Enzyme function prediction using contrastive learning
10.1126/science.adf2465 · 2023 · External reference
Robust enzyme discovery and engineering with deep-learning using CataPro
2025 · External reference
Enzyme specificity prediction using cross-attention graph neural networks
10.1038/s41586-025-09697-2 · 2025 · External reference
Automated structure- and sequence-based design of proteins for high bacterial expression and stability
10.1016/j.molcel.2016.06.012 · 2016 · External reference
Automated design of efficient and functionally diverse enzyme repertoires
10.1016/j.molcel.2018.08.033 · 2018 · External reference
An evolution-based model for designing chorismate mutase enzymes
10.1126/science.aba3304 · 2020 · External reference
Simulating 500 million years of evolution with a language model
10.1126/science.ads0018 · 2025 · External reference
ProtGPT2 is a deep unsupervised language model for protein design
10.1038/s41467-022-32007-7 · 2022 · External reference
Conditional language models enable the efficient design of proficient enzymes
2024 · External reference
De novo design of triosephosphate isomerases using generative language models
2024 · External reference
Large language models generate functional protein sequences across diverse families
10.1038/s41587-022-01618-2 · 2023 · External reference
Accelerating protein design by scaling experimental characterization
10.1038/s41467-026-76740-9 · 2026 · External reference
Rapid directed evolution guided by protein language models and epistatic interactions
10.1126/science.aea1820 · 2026 · External reference
A generalized platform for artificial intelligence-powered autonomous enzyme engineering
10.1038/s41467-025-61209-y · 2025 · External reference
Evaluation of machine learning-assisted directed evolution across diverse combinatorial landscapes
2025 · External reference
Rapid in silico directed evolution by a protein language model with EVOLVEpro
10.1126/science.adr6006 · 2025 · External reference
The Protein Design Archive (PDA): insights from 40 years of protein design
10.1038/s41587-025-02607-x · 2025 · External reference
Enzyme Engineering Database (EnzEngDB): a platform for sharing and interpreting sequence-function relationships across protein engineering campaigns
10.1093/nar/gkaf1142 · 2026 · External reference
Results of the Protein Engineering Tournament: an open science benchmark for protein modeling and design
10.1002/prot.70008 · 2025 · External reference
