AIMC Topic: 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...
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...
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) ...
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...
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...
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...
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 (...
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...
Prediction of designer-recombinases for DNA editing with generative deep learning.
Nature communications
Dec 27, 2022
Site-specific tyrosine-type recombinases are effective tools for genome engineering, with the first engineered variants having demonstrated therapeutic potential. So far, adaptation to new DNA target site selectivity of designer-recombinases has been...
Forty years of directed evolution and its continuously evolving technology toolbox: A review of the patent landscape.
Biotechnology and bioengineering
Jan 7, 2022
Generating functional protein variants with novel or improved characteristics has been a goal of the biotechnology industry and life sciences, for decades. Rational design and directed evolution are two major pathways to achieve the desired ends. Whi...
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