AIMC Topic: Molecular Dynamics Simulation

Clear Filters Showing 551 to 560 of 710 articles

Coupling dynamics and evolutionary information with structure to identify protein regulatory and functional binding sites.

Proteins Jun 22, 2019
Binding sites in proteins can be either specifically functional binding sites (active sites) that bind specific substrates with high affinity or regulatory binding sites (allosteric sites), that modulate the activity of functional binding sites throu...
Algorithms Protein Binding Evolution, Molecular Humans Artificial Intelligence Machine Learning Proteins Databases, Protein Molecular Dynamics Simulation Protein Conformation Binding Sites Allosteric Site Allosteric Regulation
View on PubMed DOI

Prediction of Sub-Monomer A2 Domain Dynamics of the von Willebrand Factor by Machine Learning Algorithm and Coarse-Grained Molecular Dynamics Simulation.

Scientific reports Jun 21, 2019
We develop a machine learning tool useful for predicting the instantaneous dynamical state of sub-monomer features within long linear polymer chains, as well as extracting the dominant macromolecular motions associated with sub-monomer behaviors of i...
Algorithms Molecular Dynamics Simulation von Willebrand Factor Protein Conformation Humans Machine Learning
View on PubMed DOI

Analysis of the Deleterious Single Nucleotide Polymorphisms Impact on Estrogen Receptor Alpha-p53 Interaction: A Machine Learning Approach.

International journal of molecular sciences Jun 18, 2019
Breast cancer is a leading cancer type and one of the major health issues faced by women around the world. Some of its major risk factors include body mass index, hormone replacement therapy, family history and germline mutations. Of these risk facto...
Mutation Molecular Dynamics Simulation Tumor Suppressor Protein p53 Polymorphism, Single Nucleotide Protein Conformation Humans Computational Biology Estrogen Receptor alpha Structure-Activity Relationship Neural Networks, Computer Protein Interaction Domains and Motifs Machine Learning Molecular Docking Simulation Protein Binding
View on PubMed DOI

Machine Learning Models Combined with Virtual Screening and Molecular Docking to Predict Human Topoisomerase I Inhibitors.

Molecules (Basel, Switzerland) Jun 4, 2019
In this work, random forest (RF), support vector machine, k-nearest neighbor and C4.5 decision tree, were used to establish classification models for predicting whether an unknown molecule is an inhibitor of human topoisomerase I (Top1) protein. All ...
Computer Simulation Reproducibility of Results Molecular Docking Simulation Humans Machine Learning Algorithms Quantitative Structure-Activity Relationship Topoisomerase I Inhibitors ROC Curve Molecular Structure Molecular Dynamics Simulation
View on PubMed DOI

A Machine Learning Approach for the Discovery of Ligand-Specific Functional Mechanisms of GPCRs.

Molecules (Basel, Switzerland) Jun 2, 2019
G protein-coupled receptors (GPCRs) play a key role in many cellular signaling mechanisms, and must select among multiple coupling possibilities in a ligand-specific manner in order to carry out a myriad of functions in diverse cellular contexts. Muc...
Humans Receptors, G-Protein-Coupled Molecular Dynamics Simulation Ligands Receptor, Serotonin, 5-HT2A Quantitative Structure-Activity Relationship Binding Sites Drug Design Drug Discovery Protein Binding Machine Learning Algorithms Molecular Docking Simulation
View on PubMed DOI

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...
Physics Materials Science Computer Simulation Molecular Dynamics Simulation Monte Carlo Method Neural Networks, Computer Machine Learning
View on PubMed DOI

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 Proteins Molecular Dynamics Simulation Thermodynamics Quantum Theory Protein Conformation Static Electricity
View on PubMed DOI

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 Docking Simulation Algorithms Proteins Deep Learning Protein Binding Molecular Dynamics Simulation Protein Conformation
View on PubMed DOI

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 ...
Computational Biology Support Vector Machine Medicine, Chinese Traditional Molecular Docking Simulation Deep Learning Protein Interaction Maps Glycogen Synthase Kinase 3 Quantitative Structure-Activity Relationship Protein Conformation Molecular Dynamics Simulation Databases, Pharmaceutical Alzheimer Disease Drug Compounding
View on PubMed DOI

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 Robotics Proprioception Equipment Design Molecular Dynamics Simulation
View on PubMed DOI
Popular Topics
Recent Journals