AIMC Topic: Biocatalysis

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Navigating the landscape of enzyme design: from molecular simulations to machine learning.

Chemical Society reviews Aug 12, 2024
Global environmental issues and sustainable development call for new technologies for fine chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the alternative to the traditional organic synthesis. However, it is c...
Molecular Dynamics Simulation Biocatalysis Machine Learning Animals Substrate Specificity Protein Engineering Enzymes Protein Conformation Enzyme Activation Humans
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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 (...
Mutation Biocatalysis Directed Molecular Evolution Machine Learning Algorithms Enzymes Protein Engineering Gene Library
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Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Scoping Review.

ACS synthetic biology Jul 24, 2024
Retrosynthesis aims to efficiently plan the synthesis of desirable chemicals by strategically breaking down molecules into readily available building block compounds. Having a long history in chemistry, retro-biosynthesis has also been used in the fi...
Synthetic Biology Biocatalysis Biosynthetic Pathways Artificial Intelligence
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ALDELE: All-Purpose Deep Learning Toolkits for Predicting the Biocatalytic Activities of Enzymes.

Journal of chemical information and modeling Apr 4, 2024
Rapidly predicting enzyme properties for catalyzing specific substrates is essential for identifying potential enzymes for industrial transformations. The demand for sustainable production of valuable industry chemicals utilizing biological resources...
Protein Conformation Enzymes Models, Molecular Biocatalysis Deep Learning
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Raman spectroscopy and one-dimensional convolutional neural network modeling as a real-time monitoring tool for in vitro transaminase-catalyzed synthesis of a pharmaceutically relevant amine precursor.

Biotechnology progress Mar 27, 2024
Raman spectroscopy has been used to measure the concentration of a pharmaceutically relevant model amine intermediate for positive allosteric modulators of nicotinic acetylcholine receptor in a ω-transaminase-catalyzed conversion. A model based on a ...
Biocatalysis Amines Transaminases Neural Networks, Computer Spectrum Analysis, Raman
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Enzyme function prediction using contrastive learning.

Science (New York, N.Y.) Mar 30, 2023
Enzyme function annotation is a fundamental challenge, and numerous computational tools have been developed. However, most of these tools cannot accurately predict functional annotations, such as enzyme commission (EC) number, for less-studied protei...
Enzymes Sequence Analysis, Protein Genomics Computational Biology Algorithms Biocatalysis Reproducibility of Results Proteins Molecular Sequence Annotation Machine Learning
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De novo design of luciferases using deep learning.

Nature Feb 22, 2023
De novo enzyme design has sought to introduce active sites and substrate-binding pockets that are predicted to catalyse a reaction of interest into geometrically compatible native scaffolds, but has been limited by a lack of suitable protein structur...
Catalytic Domain Enzyme Stability Hot Temperature Substrate Specificity Luciferases Biocatalysis Oxidation-Reduction Luminescence Luciferins Deep Learning
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Machine Learning for Prediction, Classification, and Identification of Immobilized Enzymes for Biocatalysis.

Pharmaceutical research Jan 18, 2023
BACKGROUND: Enzyme immobilization is a beneficial component involved in biocatalytic strategies. Understanding and evaluating the enzyme immobilization system plays an important role in the successful development and implementation of the biocatalysi...
Machine Learning Biocatalysis Enzymes, Immobilized Least-Squares Analysis Discriminant Analysis
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Machine Learning and Chemical Imaging to Elucidate Enzyme Immobilization for Biocatalysis.

Analytical chemistry Aug 24, 2021
Biocatalysis has rapidly become an essential tool in the scientific and industrial communities for the development of efficient, safe, and sustainable chemical syntheses. Immobilization of the biocatalyst, typically an engineered enzyme, offers signi...
Enzymes, Immobilized Machine Learning Biocatalysis Chemical Phenomena Enzyme Stability
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A hierarchical deep learning based approach for multi-functional enzyme classification.

Protein science : a publication of the Protein Society Jun 28, 2021
Enzymes are critical proteins in every organism. They speed up essential chemical reactions, help fight diseases, and have a wide use in the pharmaceutical and manufacturing industries. Wet lab experiments to figure out an enzyme's function are time ...
Terminology as Topic Enzymes Datasets as Topic Biocatalysis Deep Learning Structure-Activity Relationship
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