High-throughput screening, next generation sequencing and machine learning: advanced methods in enzyme engineering

Highly accurate protein structure prediction with AlphaFold

(2021) John Jumper et al.   NATURE

Enhancement of protein thermostability by three consecutive mutations using loop-walking method and machine learning

(2021) Kazunori Yoshida et al.   Scientific Reports

Computational Enzyme Engineering Pipelines for Optimized Production of Renewable Chemicals

(2021) Marc Scherer et al.   Frontiers in Bioengineering and Biotechnology

Development of an Improved Peroxidase-Based High-Throughput Screening for the Optimization of D-Glycerate Dehydratase Activity

(2020) Benjamin Begander et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Improved protein structure prediction using potentials from deep learning

(2020) Andrew W. Senior et al.   NATURE

A High-Throughput Screening System Based on Droplet Microfluidics for Glucose Oxidase Gene Libraries

(2020) Radivoje Prodanović et al.   MOLECULES

Comprehensive exploration of the translocation, stability and substrate recognition requirements in VIM-2 lactamase

(2020) John Z Chen et al.   eLife

Analytical description of the lag phase in coupled-enzyme substrate assays

(2020) Willem Van Roy et al.   BIOCHEMICAL ENGINEERING JOURNAL

Machine Learning Enables Selection of Epistatic Enzyme Mutants for Stability Against Unfolding and Detrimental Aggregation

(2020) Guangyue Li et al.   CHEMBIOCHEM

The AbDesign computational pipeline for modular backbone assembly and design of binders and enzymes

(2020) Rosalie Lipsh‐Sokolik et al.   PROTEIN SCIENCE

Genetically encoded stimuli-responsive cytoprotective hydrogel capsules for single cells provide novel genotype-phenotype linkage

(2019) Rosario Vanella et al.   CHEMISTRY OF MATERIALS

Machine Learning Identifies Chemical Characteristics That Promote Enzyme Catalysis

(2019) Brian M. Bonk et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Engineered Aminoacyl-tRNA Synthetases with Improved Selectivity toward Noncanonical Amino Acids

(2019) Hui Si Kwok et al.   ACS Chemical Biology

Enzyme‐mediated hydrogel encapsulation of single cells for high‐throughput screening and directed evolution of oxidoreductases

(2019) Rosario Vanella et al.   BIOTECHNOLOGY AND BIOENGINEERING

Machine learning-assisted directed protein evolution with combinatorial libraries

(2019) Zachary Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Machine learning applied to predicting microorganism growth temperatures and enzyme catalytic optima

(2019) Gang Li et al.   ACS Synthetic Biology

The Crucial Role of Methodology Development in Directed Evolution of Selective Enzymes

(2019) Ge Qu et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Machine-learning-guided directed evolution for protein engineering

(2019) Kevin K. Yang et al.   NATURE METHODS

Impact of In Vivo Protein Folding Probability on Local Fitness Landscapes

(2019) Matthew S Faber et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ultrahigh-throughput screening enables efficient single-round oxidase remodelling

(2019) Aaron Debon et al.   Nature Catalysis

One‐shot optimization of multiple enzyme parameters: Tailoring glucose oxidase for pH and electron mediators

(2019) Raluca Ostafe et al.   BIOTECHNOLOGY AND BIOENGINEERING

Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics

(2019) Claire N. Bedbrook et al.   NATURE METHODS

Deciphering interaction fingerprints from protein molecular surfaces using geometric deep learning

(2019) P. Gainza et al.   NATURE METHODS

Directed evolution improves the catalytic efficiency of TEV protease

(2019) Mateo I. Sanchez et al.   NATURE METHODS

Design of an in vitro biocatalytic cascade for the manufacture of islatravir

(2019) Mark A. Huffman et al.   SCIENCE

Machine Learning in Enzyme Engineering

(2019) Stanislav Mazurenko et al.   ACS Catalysis

Colorimetric Determination of Sulfate via an Enzyme Cascade for High-Throughput Detection of Sulfatase Activity

(2018) Jose G. Ortiz-Tena et al.   ANALYTICAL CHEMISTRY

Learned protein embeddings for machine learning

(2018) Kevin K Yang et al.   BIOINFORMATICS

Development of GFP-based high-throughput screening system for directed evolution of glucose oxidase

(2018) Gordana Kovačević et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Ultra-high throughput functional enrichment of large monoamine oxidase (MAO-N) libraries by fluorescence activated cell sorting

(2018) Joanna C. Sadler et al.   ANALYST

An enzyme-coupled assay enables rapid protein engineering for geraniol production in yeast

(2018) Jyun-Liang Lin et al.   BIOCHEMICAL ENGINEERING JOURNAL

Directed Evolution of a Bond-Forming Enzyme: Ultrahigh-Throughput Screening of Microbial Transglutaminase Using Yeast Surface Display

(2018) Lukas Deweid et al.   CHEMISTRY-A EUROPEAN JOURNAL

‘Test-tube’ evolution wins Chemistry Nobel Prize

(2018) Elizabeth Gibney et al.   NATURE

A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes

(2018) Frédéric Cadet et al.   Scientific Reports

Droplet-based microfluidic high-throughput screening of heterologous enzymes secreted by the yeast Yarrowia lipolytica

(2017) Thomas Beneyton et al.   Microbial Cell Factories

Trade-offs between enzyme fitness and solubility illuminated by deep mutational scanning

(2017) Justin R. Klesmith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-mutation fitness landscapes for an enzyme on multiple substrates reveal specificity is globally encoded

(2017) Emily E. Wrenbeck et al.   Nature Communications

Machine learning to design integral membrane channelrhodopsins for efficient eukaryotic expression and plasma membrane localization

(2017) Claire N. Bedbrook et al.   PLoS Computational Biology

Deep mutational scanning of S. pyogenes Cas9 reveals important functional domains

(2017) Jeffrey M. Spencer et al.   Scientific Reports

Substrate Engineering Enabling Fluorescence Droplet Entrapment for IVC-FACS-Based Ultrahigh-Throughput Screening

(2016) Fuqiang Ma et al.   ANALYTICAL CHEMISTRY

Fully automatized high-throughput enzyme library screening using a robotic platform

(2016) Mark Dörr et al.   BIOTECHNOLOGY AND BIOENGINEERING

The Generation and Exploitation of Protein Mutability Landscapes for Enzyme Engineering

(2016) Jan-Ytzen van der Meer et al.   CHEMBIOCHEM

Enzyme- and affinity biomolecule-mediated polymerization systems for biological signal amplification and cell screening

(2016) Klara H Malinowska et al.   CURRENT OPINION IN BIOTECHNOLOGY

Ultrahigh-throughput–directed enzyme evolution by absorbance-activated droplet sorting (AADS)

(2016) Fabrice Gielen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using mutability landscapes of a promiscuous tautomerase to guide the engineering of enantioselective Michaelases

(2016) Jan-Ytzen van der Meer et al.   Nature Communications

In vitro flow cytometry-based screening platform for cellulase engineering

(2016) Georgette Körfer et al.   Scientific Reports

Quantifying Synergy, Thermostability, and Targeting of Cellulolytic Enzymes and Cellulosomes with Polymerization-Based Amplification

(2015) Klara H. Malinowska et al.   ANALYTICAL CHEMISTRY

Cell-free expression with the toxic amino acid canavanine

(2015) Emanuel G. Worst et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Evolvability as a Function of Purifying Selection in TEM-1 β-Lactamase

(2015) Michael A. Stiffler et al.   CELL

Exploring the Protein Stability Landscape:Bacillus subtilisLipase A as a Model for Detergent Tolerance

(2015) Alexander Fulton et al.   CHEMBIOCHEM

Activity-Fed Translation (AFT) Assay: A New High-Throughput Screening Strategy for Enzymes in Droplets

(2015) Gabrielle Woronoff et al.   CHEMBIOCHEM

Liposome-Based in Vitro Evolution of Aminoacyl-tRNA Synthetase for Enhanced Pyrrolysine Derivative Incorporation

(2015) Atsuko Uyeda et al.   CHEMBIOCHEM

A flow cytometer-based whole cell screening toolbox for directed hydrolase evolution through fluorescent hydrogels

(2015) Nina Lülsdorf et al.   CHEMICAL COMMUNICATIONS

In-Depth High-Throughput Screening of Protein Engineering Libraries by Split-GFP Direct Crude Cell Extract Data Normalization

(2015) Javier Santos-Aberturas et al.   CHEMISTRY & BIOLOGY

High-throughput analysis and protein engineering using microcapillary arrays

(2015) Bob Chen et al.   Nature Chemical Biology

Ultra-High-Throughput Screening of an In Vitro-Synthesized Horseradish Peroxidase Displayed on Microbeads Using Cell Sorter

(2015) Bo Zhu et al.   PLoS One

Dissecting enzyme function with microfluidic-based deep mutational scanning

(2015) Philip A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Sequence-Flux Mapping of a Levoglucosan Utilization Pathway in E. coli

(2015) Justin R. Klesmith et al.   ACS Synthetic Biology

A Competitive Flow Cytometry Screening System for Directed Evolution of Therapeutic Enzyme

(2015) Feng Cheng et al.   ACS Synthetic Biology

One in a Million: Flow Cytometric Sorting of Single Cell-Lysate Assays in Monodisperse Picolitre Double Emulsion Droplets for Directed Evolution

(2014) Anastasia Zinchenko et al.   ANALYTICAL CHEMISTRY

A high-throughput cellulase screening system based on droplet microfluidics

(2014) Raluca Ostafe et al.   Biomicrofluidics

Directed evolution of an exoglucanase facilitated by a co-expressed β-glucosidase and construction of a whole engineered cellulase system in Escherichia coli

(2014) Min Liu et al.   BIOTECHNOLOGY LETTERS

A Fluorescent Hydrogel-Based Flow Cytometry High-Throughput Screening Platform for Hydrolytic Enzymes

(2014) Christian Pitzler et al.   CHEMISTRY & BIOLOGY

Ultra-High-Throughput Screening Method for the Directed Evolution of Glucose Oxidase

(2014) Raluca Ostafe et al.   CHEMISTRY & BIOLOGY

Redox-Initiated Hydrogel System for Detection and Real-Time Imaging of Cellulolytic Enzyme Activity

(2014) Klara H. Malinowska et al.   ChemSusChem

A Comprehensive, High-Resolution Map of a Gene’s Fitness Landscape

(2014) Elad Firnberg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Deep mutational scanning: a new style of protein science

(2014) Douglas M Fowler et al.   NATURE METHODS

Comprehensive mutational scanning of a kinasein vivoreveals substrate-dependent fitness landscapes

(2014) Alexandre Melnikov et al.   NUCLEIC ACIDS RESEARCH

Reprogramming the specificity of sortase enzymes

(2014) Brent M. Dorr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Directed co-evolution of an endoglucanase and a β-glucosidase in Escherichia coli by a novel high-throughput screening method

(2013) Min Liu et al.   CHEMICAL COMMUNICATIONS

Navigating the protein fitness landscape with Gaussian processes

(2013) P. A. Romero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Capturing the mutational landscape of the beta-lactamase TEM-1

(2013) H. Jacquier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Engineering of TEV protease variants by yeast ER sequestration screening (YESS) of combinatorial libraries

(2013) L. Yi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Activity-enhancing mutations in an E3 ubiquitin ligase identified by high-throughput mutagenesis

(2013) L. M. Starita et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Flow cytometry-based ultra-high-throughput screening assay for cellulase activity

(2012) Raluca Ostafe et al.   ANALYTICAL BIOCHEMISTRY

Ultrahigh Throughput Screening System for Directed Glucose Oxidase Evolution in Yeast Cells

(2012) Radivoje Prodanovic et al.   COMBINATORIAL CHEMISTRY & HIGH THROUGHPUT SCREENING

Deep Sequencing of Systematic Combinatorial Libraries Reveals β-Lactamase Sequence Constraints at High Resolution

(2012) Zhifeng Deng et al.   JOURNAL OF MOLECULAR BIOLOGY

A completely in vitro ultrahigh-throughput droplet-based microfluidic screening system for protein engineering and directed evolution

(2012) Ali Fallah-Araghi et al.   LAB ON A CHIP

Flow Cytometer-Based High-Throughput Screening System for Accelerated Directed Evolution of P450 Monooxygenases

(2012) Anna Joëlle Ruff et al.   ACS Catalysis

Ultrahigh-throughput screening in drop-based microfluidics for directed evolution

(2010) J. J. Agresti et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fluorescence-activated droplet sorting (FADS): efficient microfluidic cell sorting based on enzymatic activity

(2009) Jean-Christophe Baret et al.   LAB ON A CHIP

Single-Cell High-Throughput Screening To Identify Enantioselective Hydrolytic Enzymes

(2008) Stefan Becker et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Engineering Hyperthermostability into a GH11 Xylanase Is Mediated by Subtle Changes to Protein Structure

(2008) Claire Dumon et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Enzyme optimization: moving from blind evolution to statistical exploration of sequence–function space

(2008) Richard J. Fox et al.   TRENDS IN BIOTECHNOLOGY