AIMC Topic: Molecular Dynamics Simulation

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Physicochemical property based computational scheme for classifying DNA sequence elements of Saccharomyces cerevisiae.

Computational biology and chemistry Dec 26, 2018
GenerationE of huge "omics" data necessitates the development and application of computational methods to annotate the data in terms of biological features. In the context of DNA sequence, it is important to unravel the hidden physicochemical signatu...
DNA Computational Biology Molecular Dynamics Simulation Chemistry, Physical Hydrogen Bonding Sequence Analysis, DNA Saccharomyces cerevisiae
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Toward Achieving Efficient and Accurate Ligand-Protein Unbinding with Deep Learning and Molecular Dynamics through RAVE.

Journal of chemical theory and computation Dec 24, 2018
In this work, we demonstrate how to leverage our recent iterative deep learning-all atom molecular dynamics (MD) technique "Reweighted autoencoded variational Bayes for enhanced sampling (RAVE)" (Ribeiro, Bravo, Wang, Tiwary, J. Chem. Phys. 2018, 149...
Molecular Dynamics Simulation Ligands Thermodynamics Deep Learning Protein Binding Proteins
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Combined molecular dynamics and neural network method for predicting protein antifreeze activity.

Proceedings of the National Academy of Sciences of the United States of America Dec 7, 2018
Antifreeze proteins (AFPs) are a diverse class of proteins that depress the kinetically observable freezing point of water. AFPs have been of scientific interest for decades, but the lack of an accurate model for predicting AFP activity has hindered ...
Protein Conformation Thermodynamics Antifreeze Proteins Crystallization Freezing Animals Humans Water Neural Networks, Computer Models, Theoretical Temperature Kinetics Molecular Dynamics Simulation
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RNA3DCNN: Local and global quality assessments of RNA 3D structures using 3D deep convolutional neural networks.

PLoS computational biology Nov 27, 2018
Quality assessment is essential for the computational prediction and design of RNA tertiary structures. To date, several knowledge-based statistical potentials have been proposed and proved to be effective in identifying native and near-native RNA st...
RNA Datasets as Topic Hot Temperature Neural Networks, Computer Molecular Dynamics Simulation Nucleic Acid Conformation Monte Carlo Method
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Thermodynamic integration network approach to ion transport through protein channels: Perspectives and limits.

Journal of computational chemistry Oct 11, 2018
We present a molecular dynamics simulation study of alkali metal cation transport through the double-helical and the head-to-head conformers of the gramicidin ion channel. Our approach is based on a thermodynamic integration network, which consists o...
Molecular Dynamics Simulation Protein Conformation Thermodynamics Ion Transport Least-Squares Analysis Ion Channels Neural Networks, Computer
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Predicting Thermodynamic Properties of Alkanes by High-Throughput Force Field Simulation and Machine Learning.

Journal of chemical information and modeling Sep 26, 2018
Knowledge of the thermodynamic properties of molecules is essential for chemical process design and the development of new materials. Experimental measurements are often expensive and not environmentally friendly. In the past, studies using molecular...
Molecular Dynamics Simulation High-Throughput Screening Assays Thermodynamics Alkanes Machine Learning Temperature Models, Chemical Neural Networks, Computer
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Predicting improved protein conformations with a temporal deep recurrent neural network.

PloS one Sep 4, 2018
Accurate protein structure prediction from amino acid sequence is still an unsolved problem. The most reliable methods centre on template based modelling. However, the accuracy of these models entirely depends on the availability of experimentally re...
Amino Acid Sequence Protein Conformation Protein Folding Deep Learning Molecular Dynamics Simulation Sequence Analysis, Protein Neural Networks, Computer Software Algorithms
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Comparison of response surface methodology and artificial neural network to optimize novel ophthalmic flexible nano-liposomes: Characterization, evaluation, in vivo pharmacokinetics and molecular dynamics simulation.

Colloids and surfaces. B, Biointerfaces Aug 23, 2018
To improve the topical delivery of pilocarpine hydrochloride (PN) to treat glaucoma, flexible nano-liposomes containing PN (PN-FLs) were prepared, optimized and characterized. Artificial neural network (ANN) and response surface methodology (RSM) wer...
Spectroscopy, Fourier Transform Infrared Particle Size Ophthalmic Solutions Molecular Dynamics Simulation Rabbits Neural Networks, Computer Animals Nanoparticles Static Electricity Pilocarpine Drug Liberation Thermodynamics Liposomes Irritants
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Transferable Dynamic Molecular Charge Assignment Using Deep Neural Networks.

Journal of chemical theory and computation Aug 17, 2018
The ability to accurately and efficiently compute quantum-mechanical partial atomistic charges has many practical applications, such as calculations of IR spectra, analysis of chemical bonding, and classical force field parametrization. Machine learn...
Neural Networks, Computer Proteins Models, Chemical Spectrophotometry, Infrared Methanol Molecular Dynamics Simulation
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Linking of single-molecule experiments with molecular dynamics simulations by machine learning.

eLife May 3, 2018
Single-molecule experiments and molecular dynamics (MD) simulations are indispensable tools for investigating protein conformational dynamics. The former provide data, such as donor-acceptor distances, whereas the latter give atomistic information, ...
Single Molecule Imaging Protein Folding Molecular Dynamics Simulation Machine Learning Fluorescence Resonance Energy Transfer Carrier Proteins Protein Conformation
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