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Opportunities and challenges for machine learning-assisted enzyme engineering
Enzymes can be engineered at the level of their amino acid sequences to optimize key
properties such as expression, stability, substrate range, and catalytic efficiency─ or even to …
properties such as expression, stability, substrate range, and catalytic efficiency─ or even to …
Exploring protein fitness landscapes by directed evolution
Directed evolution circumvents our profound ignorance of how a protein's sequence
encodes its function by using iterative rounds of random mutation and artificial selection to …
encodes its function by using iterative rounds of random mutation and artificial selection to …
Machine learning-assisted directed protein evolution with combinatorial libraries
To reduce experimental effort associated with directed protein evolution and to explore the
sequence space encoded by mutating multiple positions simultaneously, we incorporate …
sequence space encoded by mutating multiple positions simultaneously, we incorporate …
Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently
The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …
ability to modify the sequence, and hence the structure and activity, of individual proteins in …
DIMPLE: deep insertion, deletion, and missense mutation libraries for exploring protein variation in evolution, disease, and biology
Insertions and deletions (indels) enable evolution and cause disease. Due to technical
challenges, indels are left out of most mutational scans, limiting our understanding of them in …
challenges, indels are left out of most mutational scans, limiting our understanding of them in …
Protein stability promotes evolvability
JD Bloom, ST Labthavikul, CR Otey… - Proceedings of the …, 2006 - pnas.org
The biophysical properties that enable proteins to so readily evolve to perform diverse
biochemical tasks are largely unknown. Here, we show that a protein's capacity to evolve is …
biochemical tasks are largely unknown. Here, we show that a protein's capacity to evolve is …
Laboratory evolution of stereoselective enzymes: a prolific source of catalysts for asymmetric reactions
MT Reetz - Angewandte Chemie International Edition, 2011 - Wiley Online Library
Asymmetric catalysis plays a key role in modern synthetic organic chemistry, with synthetic
catalysts and enzymes being the two available options. During the latter part of the last …
catalysts and enzymes being the two available options. During the latter part of the last …
Addressing the numbers problem in directed evolution
MT Reetz, D Kahakeaw, R Lohmer - ChemBioChem, 2008 - Wiley Online Library
Our previous contribution to increasing the efficiency of directed evolution is iterative
saturation mutagenesis (ISM) as a systematic means of generating focused libraries for the …
saturation mutagenesis (ISM) as a systematic means of generating focused libraries for the …
Evolving artificial metalloenzymes via random mutagenesis
Random mutagenesis has the potential to optimize the efficiency and selectivity of protein
catalysts without requiring detailed knowledge of protein structure; however, introducing …
catalysts without requiring detailed knowledge of protein structure; however, introducing …
Ultrahigh‐throughput FACS‐based screening for directed enzyme evolution
Directed enzyme evolution has proven to be a powerful tool for improving a range of
properties of enzymes through consecutive rounds of diversification and selection. However …
properties of enzymes through consecutive rounds of diversification and selection. However …