AIMC Topic: Molecular Dynamics Simulation

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AMARO: All Heavy-Atom Transferable Neural Network Potentials of Protein Thermodynamics.

Journal of chemical theory and computation Nov 8, 2024
All-atom molecular simulations offer detailed insights into macromolecular phenomena, but their substantial computational cost hinders the exploration of complex biological processes. We introduce Advanced Machine-learning Atomic Representation Omni-...
Molecular Dynamics Simulation Neural Networks, Computer Thermodynamics Machine Learning Proteins
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Molecular mechanism underlying effect of D93 and D289 protonation states on inhibitor-BACE1 binding: exploration from multiple independent Gaussian accelerated molecular dynamics and deep learning.

SAR and QSAR in environmental research Nov 8, 2024
BACE1 has been regarded as an essential drug design target for treating Alzheimer's disease (AD). Multiple independent Gaussian accelerated molecular dynamics simulations (GaMD), deep learning (DL), and molecular mechanics general Born surface area (...
Quantitative Structure-Activity Relationship Molecular Dynamics Simulation Protons Drug Design Amyloid Precursor Protein Secretases Hydrogen Bonding Aspartic Acid Endopeptidases Deep Learning
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Small molecule inhibitors of IL-1R1/IL-1β interaction identified via transfer machine learning QSAR modelling.

International journal of biological macromolecules Nov 7, 2024
The human interleukin-1 receptor I (IL-1R1) is a cytokine receptor recognized by interleukin 1β (IL-1β), among other cytokines. Over activation of IL-1R1 has been implicated in various inflammatory conditions. This research aims to identify small-mol...
Interleukin-1beta Molecular Dynamics Simulation Quantitative Structure-Activity Relationship Molecular Docking Simulation Small Molecule Libraries Humans Protein Binding Machine Learning Receptors, Interleukin-1 Type I
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Physics-Based Machine Learning Trains Hamiltonians and Decodes the Sequence-Conformation Relation in the Disordered Proteome.

Journal of chemical theory and computation Nov 6, 2024
Intrinsically disordered proteins and regions (IDPs) are involved in vital biological processes. To understand the IDP function, often controlled by conformation, we need to find the link between sequence and conformation. We decode this link by inte...
Proteome Molecular Dynamics Simulation Machine Learning Protein Conformation Intrinsically Disordered Proteins Static Electricity
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Ab initio characterization of protein molecular dynamics with AIBMD.

Nature Nov 6, 2024
Biomolecular dynamics simulation is a fundamental technology for life sciences research, and its usefulness depends on its accuracy and efficiency. Classical molecular dynamics simulation is fast but lacks chemical accuracy. Quantum chemistry methods...
Time Factors Proteins Molecular Dynamics Simulation Quantum Theory Density Functional Theory Artificial Intelligence Machine Learning Peptides Protein Folding Protein Conformation Thermodynamics Protein Unfolding Nuclear Magnetic Resonance, Biomolecular
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Utilizing machine learning and molecular dynamics for enhanced drug delivery in nanoparticle systems.

Scientific reports Nov 4, 2024
Materials data science and machine learning (ML) are pivotal in advancing cancer treatment strategies beyond traditional methods like chemotherapy. Nanotherapeutics, which merge nanotechnology with targeted drug delivery, exemplify this advancement b...
Drug Delivery Systems Nanoparticles Humans Molecular Dynamics Simulation Machine Learning
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Machine-Learning Approach to Identify Potential Dengue Virus Protease Inhibitors: A Computational Perspective.

The journal of physical chemistry. B Nov 1, 2024
The global prevalence of dengue virus (DENV), a widespread flavivirus, has led to varied epidemiological impacts, economic burdens, and health consequences. The alarming increase in infections is exacerbated by the absence of approved antiviral agent...
Viral Proteases Viral Protease Inhibitors Thermodynamics Protease Inhibitors Machine Learning Antiviral Agents Dengue Virus Serine Endopeptidases Molecular Dynamics Simulation
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A Bio-Inspired Magnetic Soft Robotic Fish for Efficient Solar-Energy Driven Water Purification.

Small methods Oct 24, 2024
Solar-driven water evaporation is a promising solution for global water scarcity but is still facing challenges due to its substantial energy requirements. Here, a magnetic soft robotic bionic fish is developed by combining magnetic nanoparticles (Fe...
Chitosan Robotics Magnetite Nanoparticles Water Purification Animals Hydrophobic and Hydrophilic Interactions Solar Energy Bionics Acrylic Resins Fishes Molecular Dynamics Simulation
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Pre-training strategy for antiviral drug screening with low-data graph neural network: A case study in HIV-1 K103N reverse transcriptase.

Journal of computational chemistry Oct 22, 2024
Graph neural networks (GNN) offer an alternative approach to boost the screening effectiveness in drug discovery. However, their efficacy is often hindered by limited datasets. To address this limitation, we introduced a robust GNN training framework...
Molecular Dynamics Simulation Drug Evaluation, Preclinical Reverse Transcriptase Inhibitors HIV-1 Machine Learning HIV Reverse Transcriptase Humans Molecular Docking Simulation Neural Networks, Computer Anti-HIV Agents
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Tackling APOE's structural challenges via in silico modeling in the era of neural networks: Can AlphaFold II help circumvent the problem of lacking full-length protein structure?

Archives of biochemistry and biophysics Oct 22, 2024
The APOE gene, encoding apolipoprotein E, is a predictor of longevity and age-related diseases. Despite numerous genetic studies, the data on molecular mechanisms by which apolipoprotein E affects the human phenotype remain incomplete due to the stru...
Humans Molecular Dynamics Simulation Protein Conformation Apolipoproteins E Neural Networks, Computer Molecular Docking Simulation
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