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

F Cadet, N Fontaine, G Li, J Sanchis… - Scientific reports, 2018 - nature.com
Directed evolution is an important research activity in synthetic biology and biotechnology.
Numerous reports describe the application of tedious mutation/screening cycles for the …

Recent advances in structure‐based enzyme engineering for functional reconstruction

SY Xu, L Zhou, Y Xu, HY Hong, C Dai… - Biotechnology and …, 2023 - Wiley Online Library
Structural information can help engineer enzymes. Usually, specific amino acids in particular
regions are targeted for functional reconstruction to enhance the catalytic performance …

Machine learning in enzyme engineering

S Mazurenko, Z Prokop, J Damborsky - ACS Catalysis, 2019 - ACS Publications
Enzyme engineering plays a central role in developing efficient biocatalysts for
biotechnology, biomedicine, and life sciences. Apart from classical rational design and …

Computational design gains momentum in enzyme catalysis engineering

HJ Wijma, DB Janssen - The FEBS journal, 2013 - Wiley Online Library
Computational protein design is becoming a powerful tool for tailoring enzymes for specific
biotechnological applications. When applied to existing enzymes, computational re‐design …

De novo enzymes by computational design

H Kries, R Blomberg, D Hilvert - Current opinion in chemical biology, 2013 - Elsevier
Computational enzyme design has emerged as a promising tool for generating made-to-
order biocatalysts. In addition to improving the reliability of the design cycle, current efforts in …

Machine learning-assisted enzyme engineering

NE Siedhoff, U Schwaneberg, MD Davari - Methods in enzymology, 2020 - Elsevier
Directed evolution and rational design are powerful strategies in protein engineering to tailor
enzyme properties to meet the demands in academia and industry. Traditional approaches …

Revolutionizing enzyme engineering through artificial intelligence and machine learning

N Singh, S Malik, A Gupta… - Emerging Topics in Life …, 2021 - portlandpress.com
The combinatorial space of an enzyme sequence has astronomical possibilities and
exploring it with contemporary experimental techniques is arduous and often ineffective …

Computational protein engineering: bridging the gap between rational design and laboratory evolution

A Barrozo, R Borstnar, G Marloie… - International Journal of …, 2012 - mdpi.com
Enzymes are tremendously proficient catalysts, which can be used as extracellular catalysts
for a whole host of processes, from chemical synthesis to the generation of novel biofuels …

Designing artificial enzymes by intuition and computation

V Nanda, RL Koder - Nature chemistry, 2010 - nature.com
The rational design of artificial enzymes, either by applying physico–chemical intuition of
protein structure and function or with the aid of computational methods, is a promising area …

Physics‐based enzyme design: Predicting binding affinity and catalytic activity

S Sirin, DA Pearlman… - … : Structure, Function, and …, 2014 - Wiley Online Library
Computational enzyme design is an emerging field that has yielded promising success
stories, but where numerous challenges remain. Accurate methods to rapidly evaluate …