AIMC Topic: Molecular Dynamics Simulation

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Flexible Fitting of Small Molecules into Electron Microscopy Maps Using Molecular Dynamics Simulations with Neural Network Potentials.

Journal of chemical information and modeling Mar 30, 2020
Despite significant advances in resolution, the potential for cryo-electron microscopy (EM) to be used in determining the structures of protein-drug complexes remains unrealized. Determination of accurate structures and coordination of bound ligands ...
Neural Networks, Computer Molecular Dynamics Simulation Molecular Conformation Cryoelectron Microscopy Microscopy, Electron Protein Conformation
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Artificial Intelligence and Machine learning based prediction of resistant and susceptible mutations in Mycobacterium tuberculosis.

Scientific reports Mar 26, 2020
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis (M.tb), causes highest number of deaths globally for any bacterial disease necessitating novel diagnosis and treatment strategies. High-throughput sequencing methods genera...
Humans Artificial Intelligence Drug Resistance, Multiple, Bacterial Polymorphism, Single Nucleotide Bayes Theorem Bacterial Proteins Machine Learning Algorithms Molecular Docking Simulation Mycobacterium tuberculosis Genes, Bacterial Mutation Genes, MDR Tuberculosis, Multidrug-Resistant Molecular Dynamics Simulation
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Exploring Successful Parameter Region for Coarse-Grained Simulation of Biomolecules by Bayesian Optimization and Active Learning.

Biomolecules Mar 21, 2020
Accompanied with an increase of revealed biomolecular structures owing to advancements in structural biology, the molecular dynamics (MD) approach, especially coarse-grained (CG) MD suitable for macromolecules, is becoming increasingly important for ...
Proton-Translocating ATPases Machine Learning Molecular Dynamics Simulation Protein Folding
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A Review on Applications of Computational Methods in Drug Screening and Design.

Molecules (Basel, Switzerland) Mar 18, 2020
Drug development is one of the most significant processes in the pharmaceutical industry. Various computational methods have dramatically reduced the time and cost of drug discovery. In this review, we firstly discussed roles of multiscale biomolecul...
Molecular Dynamics Simulation Molecular Docking Simulation Drug Design Drug Discovery Machine Learning
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Analysis of phthalate plasticizer migration from PVDC packaging materials to food simulants using molecular dynamics simulations and artificial neural network.

Food chemistry Feb 22, 2020
Based on the experimental data of gas chromatography-mass spectrometry, an improved artificial neural network was first established to predict the migration of 2-ethylhexyl phthalate (DEHP) plasticizer from poly(vinylidene chloride) (PVDC) into food ...
Neural Networks, Computer Temperature Food Packaging Solubility Plasticizers Food Contamination Polyvinyl Chloride Molecular Dynamics Simulation Diethylhexyl Phthalate Gas Chromatography-Mass Spectrometry
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A novel artificial intelligence protocol for finding potential inhibitors of acute myeloid leukemia.

Journal of materials chemistry. B Feb 18, 2020
There is currently no effective treatment for acute myeloid leukemia, and surgery is also ineffective as an important treatment for most tumors. Rapidly developing artificial intelligence technology can be applied to different aspects of drug develop...
Leukemia, Myeloid, Acute Drug Discovery Protein Binding Ligands Databases, Chemical Molecular Dynamics Simulation STAT3 Transcription Factor Humans Artificial Intelligence Machine Learning
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Machine learning approaches for analyzing and enhancing molecular dynamics simulations.

Current opinion in structural biology Jan 20, 2020
Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex biophysical systems...
Machine Learning Software Algorithms Neural Networks, Computer Models, Theoretical Molecular Dynamics Simulation
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Characterizing Protein-Ligand Binding Using Atomistic Simulation and Machine Learning: Application to Drug Resistance in HIV-1 Protease.

Journal of chemical theory and computation Jan 16, 2020
Over the past several decades, atomistic simulations of biomolecules, whether carried out using molecular dynamics or Monte Carlo techniques, have provided detailed insights into their function. Comparing the results of such simulations for a few clo...
Hydrogen Bonding Static Electricity Monte Carlo Method Mutation Molecular Dynamics Simulation HIV-1 HIV Protease Ligands Humans HIV Protease Inhibitors Drug Resistance, Viral Machine Learning Protein Binding
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Latest trends in structure based drug design with protein targets.

Advances in protein chemistry and structural biology Dec 18, 2019
Structure based drug designing is an important endeavor in the field of structural bioinformatics. Previously the entire process was dependent on the wet-lab experiments to build libraries of ligand molecules. And the molecules used to be tested to d...
Drugs, Investigational Anti-HIV Agents Ligands Molecular Docking Simulation Neuroprotective Agents Binding Sites Protein Binding Humans Structure-Activity Relationship Drug Design Computational Biology Machine Learning Proteins Thermodynamics Antineoplastic Agents Molecular Dynamics Simulation Anti-Bacterial Agents
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Integrated structural modeling and super-resolution imaging resolve GPCR oligomers.

Progress in molecular biology and translational science Dec 6, 2019
Formation of G protein-coupled receptors (GPCRs) dimers and higher order oligomers represents a key mechanism in pleiotropic signaling, yet how individual protomers function within oligomers remains poorly understood. For the Class A/rhodopsin subfam...
Protein Interaction Mapping Protein Structure, Secondary Protein Multimerization Allosteric Site Ligands Humans Fluorescence Resonance Energy Transfer Animals Receptors, G-Protein-Coupled Neural Networks, Computer Crystallography, X-Ray Protein Binding Machine Learning Computational Biology Mutation Software Molecular Dynamics Simulation Support Vector Machine Algorithms
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