AIMC Topic: 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 Mutation Molecular Dynamics Simulation Allosteric Regulation Signal Transduction Proteins
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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...
Antiviral Agents Molecular Dynamics Simulation Protease Inhibitors Peptide Hydrolases Humans Quantitative Structure-Activity Relationship Molecular Docking Simulation Coronavirus 3C Proteases COVID-19 Pandemics SARS-CoV-2 Deep Learning
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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...
Quantum Theory Solvents Cyclic N-Oxides Reproducibility of Results Spectrum Analysis Molecular Dynamics Simulation Artificial Intelligence
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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...
Collagen Amino Acid Sequence Biocompatible Materials Deep Learning Molecular Dynamics Simulation Humans
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Are Deep Learning Structural Models Sufficiently Accurate for Free-Energy Calculations? Application of FEP+ to AlphaFold2-Predicted Structures.

Journal of chemical information and modeling Sep 13, 2022
The availability of AlphaFold2 has led to great excitement in the scientific community─particularly among drug hunters─due to the ability of the algorithm to predict protein structures with high accuracy. However, beyond globally accurate protein str...
Ligands Thermodynamics Proteins Molecular Dynamics Simulation Models, Structural Prospective Studies Deep Learning Protein Binding
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On Sampling Minimum Energy Path.

Journal of chemical theory and computation Sep 8, 2022
Sampling the minimum energy path (MEP) between two minima of a system is often hindered by the presence of an energy barrier separating the two metastable states. As a consequence, direct sampling based on molecular dynamics or Markov Chain Monte Car...
Algorithms Molecular Dynamics Simulation Monte Carlo Method Neural Networks, Computer Thermodynamics
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gr Predictor: A Deep Learning Model for Predicting the Hydration Structures around Proteins.

Journal of chemical information and modeling Sep 6, 2022
Among the factors affecting biological processes such as protein folding and ligand binding, hydration, which is represented by a three-dimensional water site distribution function around the protein, is crucial. The typical methods for computing the...
Molecular Dynamics Simulation Thermodynamics Ligands Water Deep Learning Proteins
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Prediction of Potential Commercially Available Inhibitors against SARS-CoV-2 by Multi-Task Deep Learning Model.

Biomolecules Aug 21, 2022
The outbreak of COVID-19 caused millions of deaths worldwide, and the number of total infections is still rising. It is necessary to identify some potentially effective drugs that can be used to prevent the development of severe symptoms, or even dea...
Antiviral Agents Molecular Dynamics Simulation Molecular Docking Simulation COVID-19 Drug Treatment Humans Deep Learning Protease Inhibitors SARS-CoV-2
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AlphaFold, Artificial Intelligence (AI), and Allostery.

The journal of physical chemistry. B Aug 17, 2022
AlphaFold has burst into our lives. A powerful algorithm that underscores the strength of biological sequence data and artificial intelligence (AI). AlphaFold has appended projects and research directions. The database it has been creating promises a...
Molecular Dynamics Simulation Intrinsically Disordered Proteins Humans Artificial Intelligence Allosteric Regulation Protein Conformation Protein Folding
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