AIMC Topic: Enzymes

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AI-driven de novo enzyme design: Strategies, applications, and future prospects.

Biotechnology advances Sep 1, 2025
Enzymes are indispensable for biological processes and diverse applications across industries. While top-down modification strategies, such as directed evolution, have achieved remarkable success in optimizing existing enzymes, bottom-up de novo enzy...
Protein Engineering Enzymes Artificial Intelligence
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Bioinspired rational design of nanozymes.

Materials horizons Aug 11, 2025
Nanozymes, an emerging class of artificial enzymes, have attracted increasing attention for their potential in environmental monitoring, industrial catalysis, food safety, and biomedicine. To date, more than 1500 nanomaterials have been identified wi...
Catalysis Machine Learning Enzymes Nanostructures
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DeepMolecules: a web server for predicting enzyme and transporter-small molecule interactions.

Nucleic acids research Jul 7, 2025
DeepMolecules is an easily accessible web server for predicting protein-small molecule interactions. It integrates four state-of-the-art models: ESP and SPOT for identifying substrates of enzymes and transporters, respectively, TurNuP for predicting ...
Deep Learning Internet Software Small Molecule Libraries Enzymes Membrane Transport Proteins Kinetics
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A multimodal deep learning framework for enzyme turnover prediction with missing modality.

Computers in biology and medicine Jul 1, 2025
Accurate prediction of the turnover number (k), which quantifies the maximum rate of substrate conversion at an enzyme's active site, is essential for assessing catalytic efficiency and understanding biochemical reaction mechanisms. Traditional wet-l...
Enzymes Deep Learning
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DeepMBEnzy: An AI-Driven Database of Mycotoxin Biotransformation Enzymes.

Journal of agricultural and food chemistry May 28, 2025
Mycotoxins are toxic fungal metabolites that pose significant health risks. Enzyme biotransformation is a promising option for detoxifying mycotoxins and for elucidating their intracellular metabolism. However, few mycotoxin-biotransformation enzymes...
Mycotoxins Fungi Deep Learning Databases, Factual Fungal Proteins Enzymes Biotransformation
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Tackling a textbook example of multistep enzyme catalysis with deep learning-driven design.

Molecular cell Apr 3, 2025
Enzyme design has struggled to emulate the complexity and catalytic proficiency of natural enzymes. Lauko et al. show that with the help of deep learning, the design of serine hydrolases that rival nature's ingenuity is possible.
Enzymes Protein Engineering Catalysis Biocatalysis Deep Learning Humans
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[Intelligent mining, engineering, and design of proteins].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology Mar 25, 2025
Natural components serve the survival instincts of cells that are obtained through long-term evolution, while they often fail to meet the demands of engineered cells for efficiently performing biological functions in special industrial environments. ...
Algorithms Computational Biology Machine Learning Protein Engineering Enzymes Data Mining Proteins Artificial Intelligence
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DEKP: a deep learning model for enzyme kinetic parameter prediction based on pretrained models and graph neural networks.

Briefings in bioinformatics Mar 4, 2025
The prediction of enzyme kinetic parameters is crucial for screening enzymes with high catalytic efficiency and desired characteristics to catalyze natural or non-natural reactions. Data-driven machine learning models have been explored to reduce exp...
Enzymes Graph Neural Networks Deep Learning Kinetics Neural Networks, Computer
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Seq2Topt: a sequence-based deep learning predictor of enzyme optimal temperature.

Briefings in bioinformatics Mar 4, 2025
An accurate deep learning predictor is needed for enzyme optimal temperature (${T}_{opt}$), which quantitatively describes how temperature affects the enzyme catalytic activity. In comparison with existing models, a new model developed in this study,...
Enzymes Hydrogen-Ion Concentration Deep Learning Computational Biology Temperature
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DeepES: deep learning-based enzyme screening to identify orphan enzyme genes.

Bioinformatics (Oxford, England) Mar 4, 2025
MOTIVATION: Progress in sequencing technology has led to determination of large numbers of protein sequences, and large enzyme databases are now available. Although many computational tools for enzyme annotation were developed, sequence information i...
Software Humans Enzymes Computational Biology Molecular Sequence Annotation Multigene Family Metagenome Deep Learning
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