AIMC Topic: Hydrogen Bonding

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Practical High-Quality Electrostatic Potential Surfaces for Drug Discovery Using a Graph-Convolutional Deep Neural Network.

Journal of medicinal chemistry Sep 25, 2019
Inspecting protein and ligand electrostatic potential (ESP) surfaces in order to optimize electrostatic complementarity is a key activity in drug design. These ESP surfaces need to reflect the true electrostatic nature of the molecules, which typical...
Drug Discovery Deep Learning Protein Binding Organic Chemicals Factor Xa Hydrogen Bonding Static Electricity X-Linked Inhibitor of Apoptosis Protein Quantum Theory Ligands Datasets as Topic
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Shape-Based Generative Modeling for de Novo Drug Design.

Journal of chemical information and modeling Feb 28, 2019
In this work, we propose a machine learning approach to generate novel molecules starting from a seed compound, its three-dimensional (3D) shape, and its pharmacophoric features. The pipeline draws inspiration from generative models used in image ana...
Molecular Conformation Quantitative Structure-Activity Relationship Hydrogen Bonding Models, Molecular Machine Learning Molecular Structure Drug Design Pharmaceutical Preparations Hydrophobic and Hydrophilic Interactions
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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...
Humans Deep Learning Protein Interaction Maps Gaucher Disease Saposins Molecular Dynamics Simulation Catalytic Domain Hydrogen Bonding Enzyme Activation Protein Structure, Secondary Mutant Proteins Glucosylceramidase
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Physicochemical property based computational scheme for classifying DNA sequence elements of Saccharomyces cerevisiae.

Computational biology and chemistry Dec 26, 2018
GenerationE of huge "omics" data necessitates the development and application of computational methods to annotate the data in terms of biological features. In the context of DNA sequence, it is important to unravel the hidden physicochemical signatu...
Molecular Dynamics Simulation Chemistry, Physical Computational Biology Hydrogen Bonding Sequence Analysis, DNA Saccharomyces cerevisiae DNA
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Gaussian Process Regression Models for the Prediction of Hydrogen Bond Acceptor Strengths.

Molecular informatics Nov 25, 2018
We present two approaches for the computation of hydrogen bond acceptor strengths, one by machine-learning and one by a composite quantum-mechanical protocol, both based on the well-established pK scale and dataset. The QM calculations after a necess...
Inhibitory Concentration 50 Linear Models Databases, Chemical Quantitative Structure-Activity Relationship Machine Learning Hydrogen Bonding Normal Distribution Phosphodiesterase Inhibitors
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Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning.

Journal of biomolecular structure & dynamics Mar 2, 2018
Thrombin is a key component for chemotherapeutic and antithrombotic therapy development. As the physiologic and pathologic roles of the light chain still remain vague, here, we continue previous efforts to understand the impacts of the disease-associ...
Thrombin Allosteric Regulation Machine Learning Protein Binding Mutation Molecular Dynamics Simulation Sodium Protein Conformation Hydrogen Bonding Humans
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Knowledge-Based Conformer Generation Using the Cambridge Structural Database.

Journal of chemical information and modeling Feb 22, 2018
Fast generation of plausible molecular conformations is central to molecular modeling. This paper presents an approach to conformer generation that makes extensive use of the information available in the Cambridge Structural Database. By using geomet...
Molecular Conformation Macrocyclic Compounds Hydrogen Bonding Knowledge Bases Software Ligands Algorithms Databases, Chemical Proteins Databases, Protein Models, Molecular
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Design, synthesis, antibacterial evaluation and molecular docking studies of some new quinoxaline derivatives targeting dihyropteroate synthase enzyme.

Bioorganic chemistry Dec 5, 2017
Development of new antimicrobial agents is a good solution to overcome drug-resistance problems. From this perspective, new quinoxaline derivatives bearing various bioactive heterocyclic moieties (thiadiazoles, oxadiazoles, pyrazoles and thiazoles) w...
Gram-Positive Bacteria Levofloxacin Anti-Bacterial Agents Hydrophobic and Hydrophilic Interactions Microbial Sensitivity Tests Molecular Docking Simulation Hydrogen Bonding Catalytic Domain Protein Binding Drug Design Yersinia pestis Dihydropteroate Synthase Gram-Negative Bacteria Structure-Activity Relationship Quinoxalines Molecular Structure
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Integration of element specific persistent homology and machine learning for protein-ligand binding affinity prediction.

International journal for numerical methods in biomedical engineering Aug 16, 2017
Protein-ligand binding is a fundamental biological process that is paramount to many other biological processes, such as signal transduction, metabolic pathways, enzyme construction, cell secretion, and gene expression. Accurate prediction of protein...
Ligands Hydrogen Bonding Machine Learning Protein Binding Proteins Databases, Protein
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In silico identification of milk antihypertensive di- and tripeptides involved in angiotensin I-converting enzyme inhibitory activity.

Nutrition research (New York, N.Y.) Jul 28, 2017
Identification of bioactive milk peptides could improve food technology through improved selection of food supplements with a focus on antihypertensive properties. We hypothesized that angiotensin I-converting enzyme (ACE) inhibitory activities of mi...
Catalytic Domain Oligopeptides Angiotensin-Converting Enzyme Inhibitors Quantitative Structure-Activity Relationship Protein Conformation Animals Hydrogen Bonding Molecular Docking Simulation Peptidyl-Dipeptidase A Cattle Humans Peptide Fragments Computational Biology Dipeptides Proteolysis Dietary Supplements Hydrophobic and Hydrophilic Interactions Binding Sites Antihypertensive Agents Expert Systems Milk Proteins Models, Molecular
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