AIMC Topic: Epoxide Hydrolases

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Machine Learning Enables Selection of Epistatic Enzyme Mutants for Stability Against Unfolding and Detrimental Aggregation.

Chembiochem : a European journal of chemical biology Nov 17, 2020
Machine learning (ML) has pervaded most areas of protein engineering, including stability and stereoselectivity. Using limonene epoxide hydrolase as the model enzyme and innov'SAR as the ML platform, comprising a digital signal process, we achieved h...
Mutation Molecular Dynamics Simulation Rhodococcus Machine Learning Epoxide Hydrolases Protein Folding Protein Multimerization Limonene Protein Engineering
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Machine Learning on DNA-Encoded Libraries: A New Paradigm for Hit Finding.

Journal of medicinal chemistry Jun 11, 2020
DNA-encoded small molecule libraries (DELs) have enabled discovery of novel inhibitors for many distinct protein targets of therapeutic value. We demonstrate a new approach applying machine learning to DEL selection data by identifying active molecul...
Epoxide Hydrolases Proto-Oncogene Proteins c-kit Estrogen Receptor alpha Protein Kinase Inhibitors Small Molecule Libraries Neural Networks, Computer DNA Ligands Drug Discovery
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Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies.

Journal of chemical theory and computation Jun 4, 2020
Calculating absolute binding free energies is challenging and important. In this paper, we test some recently developed metadynamics-based methods and develop a new combination with a Hamiltonian replica-exchange approach. The methods were tested on ...
Ligands Thermodynamics Protein Structure, Tertiary Protein Binding Molecular Dynamics Simulation Epoxide Hydrolases Humans Algorithms Drug Design Machine Learning
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Novel Descriptors and Digital Signal Processing- Based Method for Protein Sequence Activity Relationship Study.

International journal of molecular sciences Nov 11, 2019
The work aiming to unravel the correlation between protein sequence and function in the absence of structural information can be highly rewarding. We present a new way of considering descriptors from the amino acids index database for modeling and pr...
Humans Glucagon-Like Peptide-2 Receptor Machine Learning Quantitative Structure-Activity Relationship Tumor Necrosis Factor-alpha Cytochrome P-450 Enzyme System Sequence Analysis, Protein Catalytic Domain Animals Epoxide Hydrolases
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A machine learning approach for reliable prediction of amino acid interactions and its application in the directed evolution of enantioselective enzymes.

Scientific reports Nov 13, 2018
Directed evolution is an important research activity in synthetic biology and biotechnology. Numerous reports describe the application of tedious mutation/screening cycles for the improvement of proteins. Recently, knowledge-based approaches have fac...
Epoxide Hydrolases Models, Molecular Mutation Catalytic Domain Aspergillus niger Machine Learning Stereoisomerism Substrate Specificity Directed Molecular Evolution
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PENG: a neural gas-based approach for pharmacophore elucidation. method design, validation, and virtual screening for novel ligands of LTA4H.

Journal of chemical information and modeling Feb 9, 2015
The pharmacophore concept is commonly employed in virtual screening for hit identification. A pharmacophore is generally defined as the three-dimensional arrangement of the structural and physicochemical features of a compound responsible for its aff...
Enzyme Inhibitors Crystallography, X-Ray Thermodynamics Ligands High-Throughput Screening Assays Reproducibility of Results Epoxide Hydrolases Models, Molecular Algorithms Protein Binding Aminopeptidases Benchmarking Humans Prospective Studies Neural Networks, Computer
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Rational Design of an Epoxide Hydrolase From Spatholobus Suberectus: Enhancing Catalytic Activity and Thermostability for Efficient (R)-Styrene Oxide Production.

Biotechnology journal Jun 1, 2025
(R)-Styrene oxide is a high-value chiral intermediate in pharmaceutical and chemical industries, yet its enantioselective synthesis remains challenging. Here, we engineered an epoxide hydrolase from Spatholobus suberectus (SsEH) to address its limita...
Protein Engineering Molecular Dynamics Simulation Enzyme Stability Epoxy Compounds Epoxide Hydrolases
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A machine learning based intramolecular potential for a flexible organic molecule.

Faraday discussions Dec 4, 2020
Quantum mechanical predictive modelling in chemistry and biology is often hindered by the long time scales and large system sizes required of the computational model. Here, we employ the kernel regression machine learning technique to construct an an...
Machine Learning Monte Carlo Method Software p38 Mitogen-Activated Protein Kinases Protein Binding Quantum Theory Thermodynamics Epoxide Hydrolases Organic Chemicals
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