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Molecular Dynamics Simulation

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Application of deep learning and molecular modeling to identify small drug-like compounds as potential HIV-1 entry inhibitors.

Journal of biomolecular structure & dynamics Apr 15, 2021
A generative adversarial autoencoder for the rational design of potential HIV-1 entry inhibitors able to block CD4-binding site of the viral envelope protein gp120 was developed. To do this, the following studies were carried out: (i) an autoencoder ...
Molecular Dynamics Simulation HIV-1 HIV Envelope Protein gp120 Deep Learning Anti-HIV Agents Molecular Docking Simulation
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Machine Learning Prediction of Allosteric Drug Activity from Molecular Dynamics.

The journal of physical chemistry letters Apr 12, 2021
Allosteric drugs have been attracting increasing interest over the past few years. In this context, it is common practice to use high-throughput screening for the discovery of non-natural allosteric drugs. While the discovery stage is supported by a ...
Biphenyl Compounds Pyrones Molecular Structure Molecular Dynamics Simulation Allosteric Regulation Coumarins Dihydropyridines Humans Machine Learning
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Machine Learning in QM/MM Molecular Dynamics Simulations of Condensed-Phase Systems.

Journal of chemical theory and computation Apr 5, 2021
Quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations have been developed to simulate molecular systems, where an explicit description of changes in the electronic structure is necessary. However, QM/MM MD simulations are ...
Machine Learning Molecular Dynamics Simulation Quantum Theory Static Electricity
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Identification of novel inhibitors of Keap1/Nrf2 by a promising method combining protein-protein interaction-oriented library and machine learning.

Scientific reports Apr 1, 2021
Protein-protein interactions (PPIs) are prospective but challenging targets for drug discovery, because screening using traditional small-molecule libraries often fails to identify hits. Recently, we developed a PPI-oriented library comprising 12,593...
Molecular Docking Simulation Drug Discovery Protein Binding Structure-Activity Relationship Ligands Protein Interaction Maps Molecular Conformation Humans Molecular Structure Machine Learning Molecular Dynamics Simulation NF-E2-Related Factor 2 Small Molecule Libraries Binding Sites Protein Interaction Mapping Kelch-Like ECH-Associated Protein 1
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ClassicalGSG: Prediction of log P using classical molecular force fields and geometric scattering for graphs.

Journal of computational chemistry Mar 30, 2021
This work examines methods for predicting the partition coefficient (log P) for a dataset of small molecules. Here, we use atomic attributes such as radius and partial charge, which are typically used as force field parameters in classical molecular ...
Databases, Chemical Neural Networks, Computer Molecular Dynamics Simulation
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Deciphering Complex Mechanisms of Resistance and Loss of Potency through Coupled Molecular Dynamics and Machine Learning.

Journal of chemical theory and computation Mar 30, 2021
Drug resistance threatens many critical therapeutics through mutations in the drug target. The molecular mechanisms by which combinations of mutations, especially those remote from the active site, alter drug binding to confer resistance are poorly u...
Mutation Machine Learning HIV Protease Molecular Dynamics Simulation Drug Resistance, Viral HIV Protease Inhibitors
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Reconstruction of ARNT PAS-B Unfolding Pathways by Steered Molecular Dynamics and Artificial Neural Networks.

Journal of chemical theory and computation Mar 29, 2021
Several experimental studies indicated that large conformational changes, including partial domain unfolding, have a role in the functional mechanisms of the basic helix loop helix Per/ARNT/SIM (bHLH-PAS) transcription factors. Recently, single-molec...
Molecular Dynamics Simulation Microscopy, Atomic Force Neural Networks, Computer Basic Helix-Loop-Helix Transcription Factors Protein Conformation Protein Unfolding
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Characterizing the function of domain linkers in regulating the dynamics of multi-domain fusion proteins by microsecond molecular dynamics simulations and artificial intelligence.

Proteins Mar 27, 2021
Multi-domain proteins are not only formed through natural evolution but can also be generated by recombinant DNA technology. Because many fusion proteins can enhance the selectivity of cell targeting, these artificially produced molecules, called mul...
Humans Artificial Intelligence Benchmarking Mutagenesis, Insertional Protein Domains Molecular Dynamics Simulation Computational Biology Protein Engineering Amino Acids Gene Expression Recombinant Fusion Proteins Pliability
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Uncertainty Quantification and Sensitivity Analysis of Partial Charges on Macroscopic Solvent Properties in Molecular Dynamics Simulations with a Machine Learning Model.

Journal of chemical information and modeling Mar 17, 2021
The molecular dynamics (MD) simulation technique is among the most broadly used computational methods to investigate atomistic phenomena in a variety of chemical and biological systems. One of the most common (and most uncertain) parametrization step...
Static Electricity Uncertainty Machine Learning Molecular Dynamics Simulation Solvents
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Target2DeNovoDrug: a novel programmatic tool for -deep learning based drug design for any target of interest.

Journal of biomolecular structure & dynamics Mar 11, 2021
The on-going data-science and Artificial Intelligence (AI) revolution offer researchers a fresh set of tools to approach structure-based drug design problems in the computer-aided drug design space. A novel programmatic tool that incorporates and de...
Deep Learning Molecular Dynamics Simulation Ligands Artificial Intelligence Drug Design
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