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Molecular Dynamics Simulation

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Probing the molecular mechanisms of α-synuclein inhibitors unveils promising natural candidates through machine-learning QSAR, pharmacophore modeling, and molecular dynamics simulations.

Molecular diversity Jul 18, 2023
Parkinson's disease is characterized by a multifactorial nature that is linked to different pathways. Among them, the abnormal deposition and accumulation of α-synuclein fibrils is considered a neuropathological hallmark of Parkinson's disease. Sever...
Humans alpha-Synuclein Molecular Dynamics Simulation Pharmacophore Quantitative Structure-Activity Relationship Biological Products Machine Learning Parkinson Disease Molecular Docking Simulation
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Impact of E484Q and L452R Mutations on Structure and Binding Behavior of SARS-CoV-2 B.1.617.1 Using Deep Learning AlphaFold2, Molecular Docking and Dynamics Simulation.

International journal of molecular sciences Jul 17, 2023
During the outbreak of COVID-19, many SARS-CoV-2 variants presented key amino acid mutations that influenced their binding abilities with angiotensin-converting enzyme 2 (hACE2) and neutralizing antibodies. For the B.1.617 lineage, there had been fea...
Molecular Docking Simulation Deep Learning COVID-19 SARS-CoV-2 Antibodies, Neutralizing Molecular Dynamics Simulation Protein Binding Mutation Humans
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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...
Humans Artificial Intelligence COVID-19 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...
Molecular Dynamics Simulation Cryoelectron Microscopy Artificial Intelligence
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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...
Molecular Dynamics Simulation Ligands Organic Cation Transport Proteins Organic Cation Transporter 1 Binding Sites Machine Learning Humans Molecular Docking Simulation Artificial Intelligence Protein Binding
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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...
Fatty Acids Machine Learning Molecular Dynamics Simulation
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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...
Temperature Deep Learning Molecular Conformation Molecular Dynamics Simulation Neural Networks, Computer
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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 Protein Kinase Inhibitors Machine Learning Molecular Dynamics Simulation Antitubercular Agents Humans Nucleoside-Phosphate Kinase Algorithms Molecular Docking Simulation Mycobacterium tuberculosis Drug Design
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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 Protein Structure, Tertiary Models, Molecular Neural Networks, Computer Molecular Dynamics Simulation Machine Learning
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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 Machine Learning Protein Binding Hydrogen Bonding Viral Envelope Proteins Molecular Dynamics Simulation Binding Sites Molecular Docking Simulation Monkeypox virus Antiviral Agents
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