AIMC Topic: Molecular Dynamics Simulation

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De novo generation of dual-target ligands for the treatment of SARS-CoV-2 using deep learning, virtual screening, and molecular dynamic simulations.

Journal of biomolecular structure & dynamics Jul 14, 2023
De novo generation of molecules with the necessary features offers a promising opportunity for artificial intelligence, such as deep generative approaches. However, creating novel compounds having biological activities toward two distinct targets con...
Artificial Intelligence COVID-19 Humans Deep Learning Molecular Dynamics Simulation Ligands SARS-CoV-2 Molecular Docking Simulation
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Computational modeling of membrane trafficking processes: From large molecular assemblies to chemical specificity.

Current opinion in cell biology Jul 12, 2023
In the last decade, molecular dynamics (MD) simulations have become an essential tool to investigate the molecular properties of membrane trafficking processes, often in conjunction with experimental approaches. The combination of MD simulations with...
Cryoelectron Microscopy Artificial Intelligence Molecular Dynamics Simulation
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Interaction of systemic drugs causing ocular toxicity with organic cation transporter: an artificial intelligence prediction.

Journal of biomolecular structure & dynamics Jun 20, 2023
Chronic disease patients (cancer, arthritis, cardiovascular diseases) undergo long-term systemic drug treatment. Membrane transporters in ocular barriers could falsely recognize these drugs and allow their trafficking into the eye from systemic circu...
Protein Binding Molecular Dynamics Simulation Machine Learning Molecular Docking Simulation Organic Cation Transport Proteins Organic Cation Transporter 1 Ligands Binding Sites Humans Artificial Intelligence
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Efficient interatomic descriptors for accurate machine learning force fields of extended molecules.

Nature communications Jun 15, 2023
Machine learning force fields (MLFFs) are gradually evolving towards enabling molecular dynamics simulations of molecules and materials with ab initio accuracy but at a small fraction of the computational cost. However, several challenges remain to b...
Machine Learning Molecular Dynamics Simulation Fatty Acids
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Rapid Prediction of a Liquid Structure from a Single Molecular Configuration Using Deep Learning.

Journal of chemical information and modeling Jun 12, 2023
Molecular dynamics simulation is an indispensable tool for understanding the collective behavior of atoms and molecules and the phases they form. Statistical mechanics provides accurate routes for predicting macroscopic properties as time-averages ov...
Deep Learning Neural Networks, Computer Molecular Conformation Molecular Dynamics Simulation Temperature
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Machine learning-based drug design for identification of thymidylate kinase inhibitors as a potential anti-Mycobacterium tuberculosis.

Journal of biomolecular structure & dynamics May 26, 2023
The rise of antibiotic-resistant Mycobacterium tuberculosis (Mtb) has reduced the availability of medications for tuberculosis therapy, resulting in increased morbidity and mortality globally. Tuberculosis spreads from the lungs to other parts of the...
Protein Binding Antitubercular Agents Machine Learning Molecular Docking Simulation Humans Algorithms Molecular Dynamics Simulation Nucleoside-Phosphate Kinase Protein Kinase Inhibitors Drug Design Mycobacterium tuberculosis
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Training Neural Network Models Using Molecular Dynamics Simulation Results to Efficiently Predict Cyclic Hexapeptide Structural Ensembles.

Journal of chemical theory and computation May 26, 2023
Cyclic peptides have emerged as a promising class of therapeutics. However, their design remains challenging, and many cyclic peptide drugs are simply natural products or their derivatives. Most cyclic peptides, including the current cyclic peptide ...
Peptides, Cyclic Models, Molecular Neural Networks, Computer Protein Structure, Tertiary Machine Learning Molecular Dynamics Simulation
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Machine learning and classical MD simulation to identify inhibitors against the P37 envelope protein of monkeypox virus.

Journal of biomolecular structure & dynamics May 23, 2023
Monkeypox virus (MPXV) outbreak is a serious public health concern that requires international attention. P37 of MPXV plays a pivotal role in DNA replication and acts as one of the promising targets for antiviral drug design. In this study, we intent...
Hydrophobic and Hydrophilic Interactions Hydrogen Bonding Viral Envelope Proteins Monkeypox virus Binding Sites Protein Binding Molecular Dynamics Simulation Molecular Docking Simulation Antiviral Agents Machine Learning
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Discovery of novel PARP-1 inhibitors using tandem studies: integrated docking, e-pharmacophore, deep learning based de novo and molecular dynamics simulation approach.

Journal of biomolecular structure & dynamics May 22, 2023
Cancer accounts for the majority of deaths worldwide, and the increasing incidence of breast cancer is a matter of grave concern. Poly (ADP-ribose) polymerase-1 (PARP-1) has emerged as an attractive target for the treatment of breast cancer as it has...
Pharmacophore Poly (ADP-Ribose) Polymerase-1 Poly(ADP-ribose) Polymerase Inhibitors Molecular Docking Simulation Deep Learning Female Molecular Dynamics Simulation Breast Neoplasms Ligands Protein Binding Humans Artificial Intelligence
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Enhanced sampling in explicit solvent by deep learning module in FSATOOL.

Journal of computational chemistry May 16, 2023
FSATOOL is an integrated molecular simulation and data analysis program. Its old molecular dynamics engine only supports simulations in vacuum or implicit solvent. In this work, we implement the well-known smooth particle mesh Ewald method for simula...
Molecular Dynamics Simulation Solvents Molecular Conformation Deep Learning
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