AIMC Topic: Molecular Dynamics Simulation

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Personal Precise Force Field for Intrinsically Disordered and Ordered Proteins Based on Deep Learning.

Journal of chemical information and modeling Dec 19, 2022
Intrinsically disordered proteins (IDPs) are proteins without a fixed three-dimensional (3D) structure under physiological conditions and are associated with Parkinson's disease, Alzheimer's disease, cancer, cardiovascular disease, amyloidosis, diabe...
Protein Conformation Protein Folding Alzheimer Disease Intrinsically Disordered Proteins Molecular Dynamics Simulation Humans Deep Learning
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Machine learning and molecular simulation ascertain antimicrobial peptide against Klebsiella pneumoniae from public database.

Computational biology and chemistry Dec 5, 2022
Antimicrobial peptides (AMPs) are short peptides with a broad spectrum of antimicrobial activity. They play a key role in the host innate immunity of many organisms. The growing threat of microorganisms resistant to antimicrobial agents and the lack ...
Molecular Dynamics Simulation Ligands Antimicrobial Peptides Molecular Docking Simulation Klebsiella pneumoniae Machine Learning Anti-Bacterial Agents
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DeepCV: A Deep Learning Framework for Blind Search of Collective Variables in Expanded Configurational Space.

Journal of chemical information and modeling Nov 29, 2022
We present (DeepCV), a computer code that provides an efficient and customizable implementation of the deep autoencoder neural network (DAENN) algorithm that has been developed in our group for computing collective variables (CVs) and can be used wi...
Algorithms Deep Learning Molecular Dynamics Simulation Neural Networks, Computer Software
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The search for new efficient inhibitors of SARS-COV-2 through the drug design developed by artificial intelligence.

Journal of biomolecular structure & dynamics Nov 24, 2022
The pandemic caused by Sars-CoV-2 is a viral infection that has generated one of the most significant health problems worldwide. Previous studies report the main protease (Mpro) as a potential target for this virus, as it is considered a crucial enzy...
Algorithms SARS-CoV-2 Artificial Intelligence COVID-19 Molecular Dynamics Simulation Protease Inhibitors Molecular Docking Simulation Drug Design Humans
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Charge Recombination Dynamics in a Metal Halide Perovskite Simulated by Nonadiabatic Molecular Dynamics Combined with Machine Learning.

The journal of physical chemistry letters Nov 11, 2022
Nonadiabatic coupling (NAC) plays a central role in driving nonadiabatic dynamics in various photophysical and photochemical processes. However, the high computational cost of NAC limits the time scale and system size of quantum dynamics simulation. ...
Machine Learning Calcium Compounds Recombination, Genetic Metals Molecular Dynamics Simulation
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Investigation of the Binding Fraction of PFAS in Human Plasma and Underlying Mechanisms Based on Machine Learning and Molecular Dynamics Simulation.

Environmental science & technology Oct 25, 2022
More than 7000 per- and polyfluorinated alkyl substances (PFAS) have been documented in the U.S. Environmental Protection Agency's CompTox Chemicals database. These PFAS can be used in a broad range of industrial and consumer applications but may pos...
Bioaccumulation Molecular Dynamics Simulation Fluorocarbons Humans Machine Learning
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Deep mutational scanning and machine learning reveal structural and molecular rules governing allosteric hotspots in homologous proteins.

eLife Oct 13, 2022
A fundamental question in protein science is where allosteric hotspots - residues critical for allosteric signaling - are located, and what properties differentiate them. We carried out deep mutational scanning (DMS) of four homologous bacterial allo...
Machine Learning Proteins Signal Transduction Mutation Molecular Dynamics Simulation Allosteric Regulation
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Development of a deep learning-based quantitative structure-activity relationship model to identify potential inhibitors against the 3C-like protease of SARS-CoV-2.

Future medicinal chemistry Sep 30, 2022
In the recent COVID-19 pandemic, SARS-CoV-2 infection spread worldwide. The 3C-like protease (3CLpro) is a promising drug target for SARS-CoV-2. We constructed a deep learning-based convolutional neural network-quantitative structure-activity relat...
Molecular Docking Simulation Peptide Hydrolases Deep Learning COVID-19 Antiviral Agents Coronavirus 3C Proteases SARS-CoV-2 Molecular Dynamics Simulation Quantitative Structure-Activity Relationship Humans Pandemics Protease Inhibitors
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Integration of Quantum Chemistry, Statistical Mechanics, and Artificial Intelligence for Computational Spectroscopy: The UV-Vis Spectrum of TEMPO Radical in Different Solvents.

Journal of chemical theory and computation Sep 27, 2022
The ongoing integration of quantum chemistry, statistical mechanics, and artificial intelligence is paving the route toward more effective and accurate strategies for the investigation of the spectroscopic properties of medium-to-large size chromopho...
Molecular Dynamics Simulation Quantum Theory Solvents Artificial Intelligence Reproducibility of Results Spectrum Analysis Cyclic N-Oxides
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Discovering design principles of collagen molecular stability using a genetic algorithm, deep learning, and experimental validation.

Proceedings of the National Academy of Sciences of the United States of America Sep 26, 2022
Collagen is the most abundant structural protein in humans, providing crucial mechanical properties, including high strength and toughness, in tissues. Collagen-based biomaterials are, therefore, used for tissue repair and regeneration. Utilizing col...
Molecular Dynamics Simulation Amino Acid Sequence Biocompatible Materials Collagen Humans Deep Learning
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