AIMC Topic: Biocatalysis

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Computer-Aided Techniques in the Engineering of Enzyme Binding Pockets: New Perspectives and Frontiers.

Journal of agricultural and food chemistry Aug 11, 2025
Enzymes, recognized for their remarkable catalytic efficiency, play a crucial role in a myriad of biochemical reactions. However, the catalytic performance of natural enzymes frequently does not meet the demands of specific applications. To address t...
Protein Conformation Binding Sites Protein Engineering Enzymes Biocatalysis
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ESM-Ezy: a deep learning strategy for the mining of novel multicopper oxidases with superior properties.

Nature communications Apr 6, 2025
The UniProt database is a valuable resource for biocatalyst discovery, yet predicting enzymatic functions remains challenging, especially for low-similarity sequences. Identifying superior enzymes with enhanced catalytic properties is even harder. To...
Databases, Protein Hydrogen-Ion Concentration Deep Learning Oxidoreductases Data Mining Biocatalysis
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Enhancing the synthesis efficiency of galacto-oligosaccharides of a β-galactosidase from Paenibacillus barengoltzii by engineering the active and distal sites.

Food chemistry Apr 4, 2025
Previously, a glycoside hydrolase (GH) family 2 β-galactosidase (PbBGal2A) from Paenibacillus barengoltzii is characterized for its high transglycosylation capability. Here, the cryo-electron microscopy (cryo-EM) structure of PbBGal2A was determined,...
Oligosaccharides beta-Galactosidase Bacterial Proteins Molecular Dynamics Simulation Galactose Biocatalysis Protein Engineering Catalytic Domain Paenibacillus
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Graphene-based FETs for advanced biocatalytic profiling: investigating heme peroxidase activity with machine learning insights.

Mikrochimica acta Mar 3, 2025
Graphene-based field-effect transistors (GFETs) are rapidly gaining recognition as powerful tools for biochemical analysis due to their exceptional sensitivity and specificity. In this study, we utilize a GFET system to explore the peroxidase-based b...
Transistors, Electronic Biocatalysis Heme Graphite Horseradish Peroxidase Machine Learning Hydrogen Peroxide
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Deep learning-driven semi-rational design in phenylalanine ammonia-lyase for enhanced catalytic efficiency.

International journal of biological macromolecules Feb 19, 2025
Phenylalanine ammonia-lyase (PAL) possesses significant potential in agriculture, industry, and the treatment of various diseases, including cancer. In particular, PAL derived from Anabaena variabilis (AvPAL) has been successfully utilized in clinica...
Deep Learning Catalysis Protein Engineering Phenylalanine Ammonia-Lyase Molecular Dynamics Simulation Anabaena variabilis Mutation Biocatalysis Kinetics
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Long-Range Electrostatics in Serine Proteases: Machine Learning-Driven Reaction Sampling Yields Insights for Enzyme Design.

Journal of chemical information and modeling Feb 10, 2025
Computational enzyme design is a promising technique for producing novel enzymes for industrial and clinical needs. A key challenge that this technique faces is to consistently achieve the desired activity. Fundamental studies of natural enzymes reve...
Static Electricity Protein Engineering Catalytic Domain Serine Proteases Quantum Theory Biocatalysis Machine Learning Models, Molecular
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Machine Learning Quantum Mechanical/Molecular Mechanical Potentials: Evaluating Transferability in Dihydrofolate Reductase-Catalyzed Reactions.

Journal of chemical theory and computation Jan 15, 2025
Integrating machine learning potentials (MLPs) with quantum mechanical/molecular mechanical (QM/MM) free energy simulations has emerged as a powerful approach for studying enzymatic catalysis. However, its practical application has been hindered by t...
Thermodynamics Tetrahydrofolate Dehydrogenase Quantum Theory Machine Learning Biocatalysis Molecular Dynamics Simulation
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BioStructNet: Structure-Based Network with Transfer Learning for Predicting Biocatalyst Functions.

Journal of chemical theory and computation Dec 20, 2024
Enzyme-substrate interactions are essential to both biological processes and industrial applications. Advanced machine learning techniques have significantly accelerated biocatalysis research, revolutionizing the prediction of biocatalytic activities...
Enzymes Machine Learning Ligands Deep Learning Biocatalysis Molecular Dynamics Simulation Algorithms
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Protein representations: Encoding biological information for machine learning in biocatalysis.

Biotechnology advances Oct 2, 2024
Enzymes offer a more environmentally friendly and low-impact solution to conventional chemistry, but they often require additional engineering for their application in industrial settings, an endeavour that is challenging and laborious. To address th...
Neural Networks, Computer Biocatalysis Enzymes Machine Learning Proteins
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On synergy between ultrahigh throughput screening and machine learning in biocatalyst engineering.

Faraday discussions Sep 11, 2024
Protein design and directed evolution have separately contributed enormously to protein engineering. Without being mutually exclusive, the former relies on computation from first principles, while the latter is a combinatorial approach based on chanc...
Biocatalysis Protein Engineering Machine Learning High-Throughput Screening Assays
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