AIMC Topic: Substrate Specificity

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Deep Learning-Driven Insights into Enzyme-Substrate Interaction Discovery.

Journal of chemical information and modeling Dec 25, 2024
Enzymes are ubiquitous catalysts with enormous application potential in biomedicine, green chemistry, and biotechnology. However, accurately predicting whether a molecule serves as a substrate for a specific enzyme, especially for novel entities, rem...
Substrate Specificity Enzymes Neural Networks, Computer Deep Learning
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Lipid discovery enabled by sequence statistics and machine learning.

eLife Dec 10, 2024
Bacterial membranes are complex and dynamic, arising from an array of evolutionary pressures. One enzyme that alters membrane compositions through covalent lipid modification is MprF. We recently identified that MprF synthesizes lysyl-phosphatidylgl...
Machine Learning Bacterial Proteins Streptococcus agalactiae Enterococcus Phosphatidylglycerols Substrate Specificity Glycolipids Lysine
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Correlating enzymatic reactivity for different substrates using transferable data-driven collective variables.

Proceedings of the National Academy of Sciences of the United States of America Nov 26, 2024
Machine learning (ML) is transforming the investigation of complex biological processes. In enzymatic catalysis, one significant challenge is identifying the reactive conformations (RC) of the enzyme:substrate complex where the substrate assumes a pr...
Machine Learning Oligosaccharides Catalytic Domain Humans Pancreatic alpha-Amylases Protein Conformation Substrate Specificity
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Deciphering Cas9 specificity: Role of domain dynamics and RNA:DNA hybrid interactions revealed through machine learning and accelerated molecular simulations.

International journal of biological macromolecules Nov 19, 2024
CRISPR/Cas9 technology is widely used for gene editing, but off-targeting still remains a major concern in therapeutic applications. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates o...
Machine Learning DNA Substrate Specificity CRISPR-Associated Protein 9 Francisella Protein Domains Molecular Dynamics Simulation RNA CRISPR-Cas Systems Bacterial Proteins
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SPOT: A machine learning model that predicts specific substrates for transport proteins.

PLoS biology Sep 26, 2024
Transport proteins play a crucial role in cellular metabolism and are central to many aspects of molecular biology and medicine. Determining the function of transport proteins experimentally is challenging, as they become unstable when isolated from ...
Substrate Specificity Machine Learning Carrier Proteins Biological Transport Software
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Prediction of Cytochrome P450 Substrates Using the Explainable Multitask Deep Learning Models.

Chemical research in toxicology Aug 28, 2024
Cytochromes P450 (P450s or CYPs) are the most important phase I metabolic enzymes in the human body and are responsible for metabolizing ∼75% of the clinically used drugs. P450-mediated metabolism is also closely associated with the formation of toxi...
Deep Learning Humans Cytochrome P-450 Enzyme System Substrate Specificity
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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...
Enzymes Substrate Specificity Protein Engineering Protein Conformation Enzyme Activation Humans Machine Learning Molecular Dynamics Simulation Animals Biocatalysis
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Uncovering substrate specificity determinants of class IIb aminoacyl-tRNA synthetases with machine learning.

Journal of molecular graphics & modelling Jul 14, 2024
Specific amino acid (AA) binding by aminoacyl-tRNA synthetases (aaRSs) is necessary for correct translation of the genetic code. Sequence and structure analyses have revealed the main specificity determinants and allowed a partitioning of aaRSs into ...
Machine Learning Amino Acid Sequence Substrate Specificity Models, Molecular Amino Acyl-tRNA Synthetases
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A multimodal Transformer Network for protein-small molecule interactions enhances predictions of kinase inhibition and enzyme-substrate relationships.

PLoS computational biology May 20, 2024
The activities of most enzymes and drugs depend on interactions between proteins and small molecules. Accurate prediction of these interactions could greatly accelerate pharmaceutical and biotechnological research. Current machine learning models des...
Humans Protein Binding Computational Biology Small Molecule Libraries Proteins Machine Learning Deep Learning Protein Kinase Inhibitors Amino Acid Sequence Substrate Specificity Protein Kinases
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De novo design of high-affinity binders of bioactive helical peptides.

Nature Dec 18, 2023
Many peptide hormones form an α-helix on binding their receptors, and sensitive methods for their detection could contribute to better clinical management of disease. De novo protein design can now generate binders with high affinity and specificity ...
Protein Structure, Secondary Glucagon Parathyroid Hormone Mass Spectrometry Substrate Specificity Proteins Deep Learning Luminescent Measurements Biosensing Techniques Diffusion Models, Molecular Peptides Computer-Aided Design
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