AIMC Topic: Enzymes

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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...
Biocatalysis Protein Conformation Animals Molecular Dynamics Simulation Protein Engineering Enzymes Humans Enzyme Activation Machine Learning Substrate Specificity
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pH-Controlled enzymatic computing for digital circuits and neural networks.

Physical chemistry chemical physics : PCCP Aug 7, 2024
Unconventional computing paradigms explore new methods for processing information beyond the capabilities of traditional electronic architectures. In this work, we present our approach to digital computation through enzymatic reactions in chemically ...
Hydrogen-Ion Concentration Enzymes Neural Networks, Computer
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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 (...
Protein Engineering Gene Library Biocatalysis Directed Molecular Evolution Enzymes Machine Learning Algorithms Mutation
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EnzyACT: A Novel Deep Learning Method to Predict the Impacts of Single and Multiple Mutations on Enzyme Activity.

Journal of chemical information and modeling Jul 22, 2024
Enzyme engineering involves the customization of enzymes by introducing mutations to expand the application scope of natural enzymes. One limitation of that is the complex interaction between two key properties, activity and stability, where the enha...
Models, Molecular Mutation Deep Learning Enzymes Protein Engineering
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ChatGPT Combining Machine Learning for the Prediction of Nanozyme Catalytic Types and Activities.

Journal of chemical information and modeling Jun 3, 2024
The design of nanozymes with superior catalytic activities is a prerequisite for broadening their biomedical applications. Previous studies have exerted significant effort in theoretical calculation and experimental trials for enhancing the catalytic...
Catalysis Machine Learning Enzymes Humans Decision Trees
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Leveraging conformal prediction to annotate enzyme function space with limited false positives.

PLoS computational biology May 29, 2024
Machine learning (ML) is increasingly being used to guide biological discovery in biomedicine such as prioritizing promising small molecules in drug discovery. In those applications, ML models are used to predict the properties of biological systems,...
Humans Enzymes Machine Learning Computational Biology Deep Learning False Positive Reactions
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Vocabulary Matters: An Annotation Pipeline and Four Deep Learning Algorithms for Enzyme Named Entity Recognition.

Journal of proteome research May 11, 2024
Enzymes are indispensable in many biological processes, and with biomedical literature growing exponentially, effective literature review becomes increasingly challenging. Natural language processing methods offer solutions to streamline this process...
Enzymes Data Mining Molecular Sequence Annotation Natural Language Processing Humans Algorithms Deep Learning
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Machine learning in nanozymes: from design to application.

Biomaterials science Apr 30, 2024
Nanozymes, a distinctive class of nanomaterials endowed with enzyme-like activity and kinetics akin to enzyme-catalysed reactions, present several advantages over natural enzymes, including cost-effectiveness, heightened stability, and adjustable act...
Machine Learning Nanostructures Enzymes Humans
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Computational scoring and experimental evaluation of enzymes generated by neural networks.

Nature biotechnology Apr 23, 2024
In recent years, generative protein sequence models have been developed to sample novel sequences. However, predicting whether generated proteins will fold and function remains challenging. We evaluate a set of 20 diverse computational metrics to ass...
Amino Acid Sequence Neural Networks, Computer Protein Engineering Algorithms Enzymes Computational Biology
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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...
Enzymes Protein Conformation Models, Molecular Deep Learning Biocatalysis
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