AIMC Topic: Molecular Dynamics Simulation

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Using molecular dynamics simulations to prioritize and understand AI-generated cell penetrating peptides.

Scientific reports May 20, 2021
Cell-penetrating peptides have important therapeutic applications in drug delivery, but the variety of known cell-penetrating peptides is still limited. With a promise to accelerate peptide development, artificial intelligence (AI) techniques includi...
Amino Acid Sequence HeLa Cells Cell Membrane Cell-Penetrating Peptides Reproducibility of Results Cell Survival Molecular Dynamics Simulation Humans Artificial Intelligence
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Treasuring the computational approach in medicinal plant research.

Progress in biophysics and molecular biology May 15, 2021
Medicinal plants serve as a valuable source of secondary metabolites since time immemorial. Computational Research in 21st century is giving more attention to medicinal plants for new drug design as pharmacological screening of bioactive compound was...
Plants, Medicinal Molecular Docking Simulation Artificial Intelligence Software Molecular Dynamics Simulation
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Integrated support vector machine and pharmacophore based virtual screening driven identification of thiophene carboxamide scaffold containing compound as potential PARP1 inhibitor.

Journal of biomolecular structure & dynamics May 5, 2021
Poly (ADP-ribose) polymerase-1 (PARP1) inhibition strategy for cancer treatment is gaining advantage particularly in patients having a mutation in BRCA1/BRCA2 gene. To date, four drugs have obtained FDA approval and some inhibitors are in clinical tr...
Humans Molecular Docking Simulation Thiophenes Quantitative Structure-Activity Relationship Poly (ADP-Ribose) Polymerase-1 Support Vector Machine Molecular Dynamics Simulation Ligands
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Deep-learning based repurposing of FDA-approved drugs against dihydrofolate reductase and molecular dynamics study.

Journal of biomolecular structure & dynamics Apr 21, 2021
causes the fatal fungal bloodstream infection in humans called Candidiasis. Most of the species are resistant to the antifungals used to treat them. Drug-resistant poses very serious public health issues. To overcome this, the development of effec...
United States Aminopyridines Candida albicans Tetrahydrofolate Dehydrogenase Humans Cyclopropanes Benzodioxoles Drug Approval Molecular Docking Simulation Rifampin Proline Molecular Dynamics Simulation Deep Learning Drug Repositioning Folic Acid Antagonists Lactams, Macrocyclic Sulfonamides Candidiasis United States Food and Drug Administration Antifungal Agents
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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 Docking Simulation Deep Learning Anti-HIV Agents HIV Envelope Protein gp120 Molecular Dynamics Simulation HIV-1
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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 ...
Allosteric Regulation Molecular Structure Molecular Dynamics Simulation Biphenyl Compounds Pyrones 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 ...
Molecular Dynamics Simulation Quantum Theory Static Electricity Machine Learning
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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 Structure Molecular Dynamics Simulation Ligands Protein Binding Structure-Activity Relationship Small Molecule Libraries Protein Interaction Mapping Kelch-Like ECH-Associated Protein 1 Molecular Conformation NF-E2-Related Factor 2 Binding Sites Humans Machine Learning Molecular Docking Simulation Drug Discovery Protein Interaction Maps
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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...
Molecular Dynamics Simulation HIV Protease Drug Resistance, Viral Machine Learning Mutation HIV Protease Inhibitors
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