AIMC Topic: Molecular Dynamics Simulation

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Physically informed artificial neural networks for atomistic modeling of materials.

Nature communications May 28, 2019
Large-scale atomistic computer simulations of materials heavily rely on interatomic potentials predicting the energy and Newtonian forces on atoms. Traditional interatomic potentials are based on physical intuition but contain few adjustable paramete...
Materials Science Monte Carlo Method Physics Neural Networks, Computer Computer Simulation Molecular Dynamics Simulation Machine Learning
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PhysNet: A Neural Network for Predicting Energies, Forces, Dipole Moments, and Partial Charges.

Journal of chemical theory and computation May 14, 2019
In recent years, machine learning (ML) methods have become increasingly popular in computational chemistry. After being trained on appropriate ab initio reference data, these methods allow for accurately predicting the properties of chemical systems,...
Neural Networks, Computer Algorithms Protein Conformation Static Electricity Thermodynamics Molecular Dynamics Simulation Quantum Theory Proteins
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Coupling Molecular Dynamics and Deep Learning to Mine Protein Conformational Space.

Structure (London, England : 1993) Apr 25, 2019
Flexibility is often a key determinant of protein function. To elucidate the link between their molecular structure and role in an organism, computational techniques such as molecular dynamics can be leveraged to characterize their conformational spa...
Molecular Dynamics Simulation Protein Conformation Protein Binding Proteins Molecular Docking Simulation Deep Learning Algorithms
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Deep Learning and Random Forest Approach for Finding the Optimal Traditional Chinese Medicine Formula for Treatment of Alzheimer's Disease.

Journal of chemical information and modeling Apr 2, 2019
It has demonstrated that glycogen synthase kinase 3β (GSK3β) is related to Alzheimer's disease (AD). On the basis of the world largest traditional Chinese medicine (TCM) database, a network-pharmacology-based approach was utilized to investigate TCM ...
Molecular Docking Simulation Support Vector Machine Medicine, Chinese Traditional Molecular Dynamics Simulation Protein Interaction Maps Computational Biology Deep Learning Glycogen Synthase Kinase 3 Quantitative Structure-Activity Relationship Protein Conformation Databases, Pharmaceutical Alzheimer Disease Drug Compounding
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Fabrication and Dynamic Modeling of Bidirectional Bending Soft Actuator Integrated with Optical Waveguide Curvature Sensor.

Soft robotics Mar 23, 2019
Soft robots exhibit many exciting properties due to their softness and body compliance. However, to interact with the environment safely and to perform a task effectively, a soft robot faces a series of challenges such as dexterous motion, propriocep...
Motion Proprioception Robotics Equipment Design Molecular Dynamics Simulation
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Automated discovery of GPCR bioactive ligands.

Current opinion in structural biology Mar 23, 2019
While G-protein-coupled receptors (GPCRs) constitute the largest class of membrane proteins, structures and endogenous ligands of a large portion of GPCRs remain unknown. Because of the involvement of GPCRs in various signaling pathways and physiolog...
Ligands Protein Conformation Molecular Docking Simulation Drug Design Machine Learning Receptors, G-Protein-Coupled Molecular Dynamics Simulation Drug Discovery Humans
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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...
Glucosylceramidase Saposins Enzyme Activation Protein Structure, Secondary Mutant Proteins Catalytic Domain Hydrogen Bonding Protein Interaction Maps Gaucher Disease Molecular Dynamics Simulation Humans Deep Learning
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Machine Learning Identifies Chemical Characteristics That Promote Enzyme Catalysis.

Journal of the American Chemical Society Feb 21, 2019
Despite tremendous progress in understanding and engineering enzymes, knowledge of how enzyme structures and their dynamics induce observed catalytic properties is incomplete, and capabilities to engineer enzymes fall far short of industrial needs. H...
Molecular Dynamics Simulation Biocatalysis Machine Learning Substrate Specificity Ketol-Acid Reductoisomerase Protein Conformation Monte Carlo Method
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Solvation Free Energy Calculations with Quantum Mechanics/Molecular Mechanics and Machine Learning Models.

The journal of physical chemistry. B Jan 15, 2019
For exploration of chemical and biological systems, the combined quantum mechanics and molecular mechanics (QM/MM) and machine learning (ML) models have been developed recently to achieve high accuracy and efficiency for molecular dynamics (MD) simul...
Quantum Theory Solvents Thermodynamics Machine Learning Molecular Dynamics Simulation
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Toward Building Protein Force Fields by Residue-Based Systematic Molecular Fragmentation and Neural Network.

Journal of chemical theory and computation Jan 7, 2019
Accurate force fields are crucial for molecular dynamics investigation of complex biological systems. Building accurate protein force fields from quantum mechanical (QM) calculations is challenging due to the complexity of proteins and high computati...
Dipeptides Static Electricity Thermodynamics Molecular Dynamics Simulation Quantum Theory Neural Networks, Computer Peptides Models, Chemical Amino Acids Proteins
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