AIMC Topic: Directed Molecular Evolution

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Machine learning-guided evolution of pyrrolysyl-tRNA synthetase for improved incorporation efficiency of diverse noncanonical amino acids.

Nature communications Jul 19, 2025
The pyrrolysyl-tRNA synthetase (PylRS) is widely used to incorporate noncanonical amino acids (ncAAs) into proteins. However, the yields of most ncAA-containing protein  remain low due to the limited activity of PylRS variants. Here, we apply machine...
Machine Learning Mutation Amino Acids Protein Engineering Codon, Terminator Amino Acyl-tRNA Synthetases Lysine Directed Molecular Evolution RNA, Transfer
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Modification and applications of glucose oxidase: optimization strategies and high-throughput screening technologies.

World journal of microbiology & biotechnology Jul 12, 2025
Glucose oxidase (GOD), an oxidoreductase (EC 1.1.3.4), catalyzes the oxidation of β-D-glucose to gluconic acid using molecular oxygen as the electron acceptor, with concomitant generation of hydrogen peroxide. Owing to its versatile catalytic propert...
Protein Engineering Gluconates Glucose High-Throughput Screening Assays Biosensing Techniques Artificial Intelligence Biotechnology Glucose Oxidase Hydrogen Peroxide Oxidation-Reduction Machine Learning Directed Molecular Evolution
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Directed Evolution of Fluorescent Genetically Encoded Biosensors: Innovative Approaches for Development and Optimization of Biosensors.

Chembiochem : a European journal of chemical biology Apr 4, 2025
Fluorescent protein-based biosensors are indispensable molecular tools in cell biology and biomedical research, providing non-invasive dynamic measurements of metabolite concentrations and other cellular signals. Traditional methods for developing th...
Biosensing Techniques Directed Molecular Evolution Luminescent Proteins Humans Machine Learning
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Advances in AAV capsid engineering: Integrating rational design, directed evolution and machine learning.

Molecular therapy : the journal of the American Society of Gene Therapy Apr 1, 2025
Adeno-associated virus (AAV) has emerged as a highly promising vector for human gene therapy due to its favorable safety profile, versatility, and ability to transduce a wide range of tissues. However, natural AAV serotypes have shortcomings, includi...
Capsid Genetic Engineering Dependovirus Transduction, Genetic Capsid Proteins Machine Learning Animals Directed Molecular Evolution Genetic Vectors Genetic Therapy Humans
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Engineering highly active nuclease enzymes with machine learning and high-throughput screening.

Cell systems Mar 12, 2025
Optimizing enzymes to function in novel chemical environments is a central goal of synthetic biology, but optimization is often hindered by a rugged fitness landscape and costly experiments. In this work, we present TeleProt, a machine learning (ML) ...
Protein Engineering Machine Learning High-Throughput Screening Assays Directed Molecular Evolution
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Development of DeepPQK and DeepQK sequence-based deep learning models to predict protein-ligand affinity and application in the directed evolution of ferulic esterase DLfae4.

International journal of biological macromolecules Mar 5, 2025
Affinity plays an essential role in the rate and stability of enzyme-catalyzed reactions, thus directly impacting the catalytic activity. In general, the predictive method for protein-ligand binding affinity mainly relies on high-resolution protein c...
Binding Sites Directed Molecular Evolution Ligands Carboxylic Ester Hydrolases Neural Networks, Computer Deep Learning Models, Molecular Amino Acid Sequence Protein Binding
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Tailoring industrial enzymes for thermostability and activity evolution by the machine learning-based iCASE strategy.

Nature communications Jan 11, 2025
The pursuit of obtaining enzymes with high activity and stability remains a grail in enzyme evolution due to the stability-activity trade-off. Here, we develop an isothermal compressibility-assisted dynamic squeezing index perturbation engineering (i...
Machine Learning Enzyme Stability Directed Molecular Evolution Evolution, Molecular Protein Engineering Enzymes
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LevSeq: Rapid Generation of Sequence-Function Data for Directed Evolution and Machine Learning.

ACS synthetic biology Dec 24, 2024
Sequence-function data provides valuable information about the protein functional landscape but is rarely obtained during directed evolution campaigns. Here, we present Long-read every variant Sequencing (LevSeq), a pipeline that combines a dual barc...
Nanopore Sequencing Software Directed Molecular Evolution Protein Engineering Machine Learning
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Machine learning-guided co-optimization of fitness and diversity facilitates combinatorial library design in enzyme engineering.

Nature communications Jul 29, 2024
The effective design of combinatorial libraries to balance fitness and diversity facilitates the engineering of useful enzyme functions, particularly those that are poorly characterized or unknown in biology. We introduce MODIFY, a machine learning (...
Enzymes Machine Learning Algorithms Directed Molecular Evolution Mutation Protein Engineering Biocatalysis Gene Library
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Machine learning and genetic algorithm-guided directed evolution for the development of antimicrobial peptides.

Journal of advanced research Mar 1, 2024
INTRODUCTION: Antimicrobial peptides (AMPs) are valuable alternatives to traditional antibiotics, possess a variety of potent biological activities and exhibit immunomodulatory effects that alleviate difficult-to-treat infections. Clarifying the stru...
Genetic Algorithms Directed Molecular Evolution Staphylococcus aureus Antimicrobial Peptides Lipopolysaccharides Anti-Bacterial Agents Machine Learning Structure-Activity Relationship Antimicrobial Cationic Peptides Penaeidae Animals Algorithms Microbial Sensitivity Tests
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