AIMC Topic: Enzymes

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DeepEnzyme: a robust deep learning model for improved enzyme turnover number prediction by utilizing features of protein 3D-structures.

Briefings in bioinformatics Jul 25, 2024
Turnover numbers (kcat), which indicate an enzyme's catalytic efficiency, have a wide range of applications in fields including protein engineering and synthetic biology. Experimentally measuring the enzymes' kcat is always time-consuming. Recently, ...
Enzymes Models, Molecular Protein Conformation Algorithms Computational Biology Deep Learning Proteins
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MPEK: a multitask deep learning framework based on pretrained language models for enzymatic reaction kinetic parameters prediction.

Briefings in bioinformatics Jul 25, 2024
Enzymatic reaction kinetics are central in analyzing enzymatic reaction mechanisms and target-enzyme optimization, and thus in biomanufacturing and other industries. The enzyme turnover number (kcat) and Michaelis constant (Km), key kinetic parameter...
Algorithms Deep Learning Kinetics Computational Biology Enzymes
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[Progress in the application of artificial intelligence-assisted molecular modification of enzymes].

Sheng wu gong cheng xue bao = Chinese journal of biotechnology Jun 25, 2024
Natural enzymes are often difficult to meet the needs of application and research in terms of activity, enantiomer selectivity or thermal stability. Therefore, it is an important task of enzyme engineering to explore efficient molecular modification ...
Protein Engineering Enzymes Artificial Intelligence
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ifDEEPre: large protein language-based deep learning enables interpretable and fast predictions of enzyme commission numbers.

Briefings in bioinformatics May 23, 2024
Accurate understanding of the biological functions of enzymes is vital for various tasks in both pathologies and industrial biotechnology. However, the existing methods are usually not fast enough and lack explanations on the prediction results, whic...
Algorithms Deep Learning Software Databases, Protein Enzymes Computational Biology Proteins
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'Set it and forget it': automated lab uses AI and robotics to improve proteins.

Nature Jan 1, 2024
Enzymes Artificial Intelligence Robotics Automation, Laboratory Enzyme Stability Temperature
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Illuminating enzyme design using deep learning.

Nature chemistry Jun 1, 2023
Enzymes Protein Conformation Deep Learning
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Data-driven enzyme engineering to identify function-enhancing enzymes.

Protein engineering, design & selection : PEDS Jan 21, 2023
Identifying function-enhancing enzyme variants is a 'holy grail' challenge in protein science because it will allow researchers to expand the biocatalytic toolbox for late-stage functionalization of drug-like molecules, environmental degradation of p...
Biocatalysis Protein Engineering Proteins Enzymes Machine Learning Catalysis
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Accelerating the optimization of enzyme-catalyzed synthesis conditions machine learning and reactivity descriptors.

Organic & biomolecular chemistry Jul 21, 2021
Enzyme-catalyzed synthesis reactions are of crucial importance for a wide range of applications. An accurate and rapid selection of optimal synthesis conditions is crucial and challenging for both human knowledge and computer predictions. In this wor...
Machine Learning Support Vector Machine Biocatalysis Enzymes
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DEEPre: sequence-based enzyme EC number prediction by deep learning.

Bioinformatics (Oxford, England) Mar 1, 2018
MOTIVATION: Annotation of enzyme function has a broad range of applications, such as metagenomics, industrial biotechnology, and diagnosis of enzyme deficiency-caused diseases. However, the time and resource required make it prohibitively expensive t...
Humans Enzymes Machine Learning Computational Biology Software Molecular Sequence Annotation
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iPTMnet: an integrated resource for protein post-translational modification network discovery.

Nucleic acids research Jan 4, 2018
Protein post-translational modifications (PTMs) play a pivotal role in numerous biological processes by modulating regulation of protein function. We have developed iPTMnet (http://proteininformationresource.org/iPTMnet) for PTM knowledge discovery, ...
Knowledge Bases Data Mining Internet Computational Biology Databases, Protein Animals Sequence Alignment Protein Processing, Post-Translational Phosphorylation Protein Interaction Maps Enzymes Humans
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