AIMC Topic: Molecular Dynamics Simulation

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Combining Molecular Dynamics and Machine Learning to Predict Self-Solvation Free Energies and Limiting Activity Coefficients.

Journal of chemical information and modeling Sep 1, 2020
Computational prediction of limiting activity coefficients is of great relevance for process design. For highly nonideal mixtures including molecules with directed interactions, methods that maintain the molecular character of the solvent are most pr...
Molecular Dynamics Simulation Solvents Thermodynamics Machine Learning
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ivis Dimensionality Reduction Framework for Biomacromolecular Simulations.

Journal of chemical information and modeling Sep 1, 2020
Molecular dynamics (MD) simulations have been widely applied to study macromolecules including proteins. However, the high dimensionality of the data sets produced by simulations makes thorough analysis difficult and further hinders a deeper understa...
Neural Networks, Computer Proteins Principal Component Analysis Molecular Dynamics Simulation
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Insights into the Kinetic Partitioning Folding Dynamics of the Human Telomeric G-Quadruplex from Molecular Simulations and Machine Learning.

Journal of chemical theory and computation Aug 25, 2020
The human telomeric DNA G-quadruplex follows a kinetic partitioning folding mechanism. The underlying folding landscape potentially has many minima separated by high free-energy barriers. However, using current theoretical models to characterize this...
Molecular Dynamics Simulation Nucleic Acid Conformation G-Quadruplexes Machine Learning Kinetics Telomere Humans
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Bayesian machine learning to discover Bruton's tyrosine kinase inhibitors.

Chemical biology & drug design Aug 18, 2020
Bruton's tyrosine kinase (BTK) has a crucial role in multiple cell signaling pathways including B-cell antigen receptor (BCR) and Fc receptor (FcR) signaling cascades, which has attracted much attention to find BTK inhibitors to treat autoimmune dise...
Protein Kinase Inhibitors Agammaglobulinaemia Tyrosine Kinase Machine Learning Reproducibility of Results Bayes Theorem Molecular Dynamics Simulation Molecular Docking Simulation Humans
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Predictive modeling by deep learning, virtual screening and molecular dynamics study of natural compounds against SARS-CoV-2 main protease.

Journal of biomolecular structure & dynamics Aug 5, 2020
The whole world is facing a great challenging time due to Coronavirus disease (COVID-19) caused by SARS-CoV-2. Globally, more than 14.6 M people have been diagnosed and more than 595 K deaths are reported. Currently, no effective vaccine or drugs are...
COVID-19 SARS-CoV-2 Molecular Docking Simulation Humans Protease Inhibitors Peptide Hydrolases Deep Learning Molecular Dynamics Simulation
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Machine Learning Force Fields and Coarse-Grained Variables in Molecular Dynamics: Application to Materials and Biological Systems.

Journal of chemical theory and computation Jul 16, 2020
Machine learning encompasses tools and algorithms that are now becoming popular in almost all scientific and technological fields. This is true for molecular dynamics as well, where machine learning offers promises of extracting valuable information ...
Proteins Molecular Dynamics Simulation Machine Learning
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Structural compliance: A new metric for protein flexibility.

Proteins Jul 14, 2020
Proteins are the active players in performing essential molecular activities throughout biology, and their dynamics has been broadly demonstrated to relate to their mechanisms. The intrinsic fluctuations have often been used to represent their dynami...
Fungal Proteins Elasticity Complement C8 Lectins Agaricales Molecular Dynamics Simulation Biomechanical Phenomena Internet Neural Networks, Computer Software Humans
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Extending the Applicability of the ANI Deep Learning Molecular Potential to Sulfur and Halogens.

Journal of chemical theory and computation Jun 29, 2020
Machine learning (ML) methods have become powerful, predictive tools in a wide range of applications, such as facial recognition and autonomous vehicles. In the sciences, computational chemists and physicists have been using ML for the prediction of ...
Thermodynamics Halogens Molecular Dynamics Simulation Sulfur Deep Learning Density Functional Theory
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Insight into potent leads for alzheimer's disease by using several artificial intelligence algorithms.

Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie Jun 16, 2020
Several proteins including S-nitrosoglutathione reductase (GSNOR), complement Factor D, complement 3b (C3b) and Protein Kinase R-like Endoplasmic Reticulum Kinase (PERK), have been demonstrated to be involved in pathogenesis pathways for Alzheimer's ...
Molecular Structure Molecular Dynamics Simulation Alzheimer Disease Cognition Signal Transduction Nootropic Agents Molecular Targeted Therapy Quantitative Structure-Activity Relationship Molecular Docking Simulation Computer-Aided Design Drug Discovery Plant Extracts Drug Design Brain Animals Humans Artificial Intelligence
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Combining Machine Learning and Enhanced Sampling Techniques for Efficient and Accurate Calculation of Absolute Binding Free Energies.

Journal of chemical theory and computation Jun 4, 2020
Calculating absolute binding free energies is challenging and important. In this paper, we test some recently developed metadynamics-based methods and develop a new combination with a Hamiltonian replica-exchange approach. The methods were tested on ...
Machine Learning Algorithms Protein Binding Molecular Dynamics Simulation Drug Design Humans Protein Structure, Tertiary Epoxide Hydrolases Ligands Thermodynamics
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