AIMC Topic: Catalytic Domain

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Profiling SARS-CoV-2 Main Protease (M) Binding to Repurposed Drugs Using Molecular Dynamics Simulations in Classical and Neural Network-Trained Force Fields.

ACS combinatorial science Oct 29, 2020
The current COVID-19 pandemic caused by a novel coronavirus SARS-CoV-2 urgently calls for a working therapeutic. Here, we report a computation-based workflow for efficiently selecting a subset of FDA-approved drugs that can potentially bind to the SA...
Neural Networks, Computer Drug Discovery Molecular Dynamics Simulation Catalytic Domain Coronavirus 3C Proteases Coronavirus Protease Inhibitors Antiviral Agents Protein Binding Drug Repositioning Workflow
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Evolutionary insights into the active-site structures of the metallo-β-lactamase superfamily from a classification study with support vector machine.

Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry Sep 18, 2020
The metallo-β-lactamase (MβL) superfamily, which is intriguing due to its enzyme promiscuity, is a good model enzyme superfamily for studies of catalytic function evolution. Our previous study traced the evolution of the phosphotriesterase activity o...
beta-Lactamases Catalytic Domain Evolution, Molecular Models, Molecular Kinetics Computational Biology Support Vector Machine
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Deep Learning Based Drug Screening for Novel Coronavirus 2019-nCov.

Interdisciplinary sciences, computational life sciences Jun 1, 2020
A novel coronavirus, called 2019-nCoV, was recently found in Wuhan, Hubei Province of China, and now is spreading across China and other parts of the world. Although there are some drugs to treat 2019-nCoV, there is no proper scientific evidence abou...
Pandemics COVID-19 SARS-CoV-2 Drug Design Humans Molecular Dynamics Simulation Drug Evaluation, Preclinical Amino Acid Sequence Coronavirus Infections Deep Learning User-Computer Interface Antiviral Agents Models, Molecular Databases, Pharmaceutical Structural Homology, Protein Betacoronavirus Pneumonia, Viral Coronavirus 3C Proteases Ligands Viral Nonstructural Proteins Catalytic Domain Databases, Nucleic Acid Oligopeptides Sequence Alignment Cysteine Endopeptidases
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Discovery of Small-Molecule Activators for Glucose-6-Phosphate Dehydrogenase (G6PD) Using Machine Learning Approaches.

International journal of molecular sciences Feb 23, 2020
Glucose-6-Phosphate Dehydrogenase (G6PD) is a ubiquitous cytoplasmic enzyme converting glucose-6-phosphate into 6-phosphogluconate in the pentose phosphate pathway (PPP). The G6PD deficiency renders the inability to regenerate glutathione due to lack...
NADP Pentose Phosphate Pathway Glucosephosphate Dehydrogenase Deficiency Drug Evaluation, Preclinical Catalytic Domain Glutathione X-Ray Diffraction Protein Interaction Domains and Motifs Glucosephosphate Dehydrogenase Molecular Docking Simulation Drug Discovery Oxidative Stress Oxidation-Reduction Humans Machine Learning Animals
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High-level expression of Thermobifida fusca glucose isomerase for high fructose corn syrup biosynthesis.

Enzyme and microbial technology Dec 13, 2019
Glucose isomerase (GIase), an efficient enzyme in the isomerization of d-glucose to d-fructose, has been widely used in food processing. In this study, an efficient expression system for a Thermobifida fusca GIase (GIase) in Escherichia coli was firs...
Catalytic Domain Fructose High Fructose Corn Syrup Recombinant Proteins Bacterial Proteins Escherichia coli Glucose Gene Expression Actinobacteria Aldose-Ketose Isomerases
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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...
Tumor Necrosis Factor-alpha Animals Cytochrome P-450 Enzyme System Catalytic Domain Quantitative Structure-Activity Relationship Sequence Analysis, Protein Epoxide Hydrolases Glucagon-Like Peptide-2 Receptor Humans Machine Learning
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De Novo Molecular Design by Combining Deep Autoencoder Recurrent Neural Networks with Generative Topographic Mapping.

Journal of chemical information and modeling Mar 5, 2019
Here we show that Generative Topographic Mapping (GTM) can be used to explore the latent space of the SMILES-based autoencoders and generate focused molecular libraries of interest. We have built a sequence-to-sequence neural network with Bidirection...
Molecular Docking Simulation Drug Design Deep Learning Small Molecule Libraries Receptor, Adenosine A2A Drug Evaluation, Preclinical Ligands Catalytic Domain
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Mechanism of glucocerebrosidase activation and dysfunction in Gaucher disease unraveled by molecular dynamics and deep learning.

Proceedings of the National Academy of Sciences of the United States of America Feb 26, 2019
The lysosomal enzyme glucocerebrosidase-1 (GCase) catalyzes the cleavage of a major glycolipid glucosylceramide into glucose and ceramide. The absence of fully functional GCase leads to the accumulation of its lipid substrates in lysosomes, causing G...
Protein Structure, Secondary Mutant Proteins Glucosylceramidase Saposins Molecular Dynamics Simulation Catalytic Domain Hydrogen Bonding Enzyme Activation Deep Learning Protein Interaction Maps Humans Gaucher Disease
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Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase.

BMC evolutionary biology Dec 22, 2018
BACKGROUND: The family of D-isomer specific 2-hydroxyacid dehydrogenases (2HADHs) contains a wide range of oxidoreductases with various metabolic roles as well as biotechnological applications. Despite a vast amount of biochemical and structural data...
Phylogeny Amino Acid Sequence Likelihood Functions Substrate Specificity Coenzymes Knowledge Bases Catalytic Domain Alcohol Oxidoreductases
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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...
Directed Molecular Evolution Epoxide Hydrolases Machine Learning Catalytic Domain Models, Molecular Stereoisomerism Mutation Substrate Specificity Aspergillus niger
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