AIMC Topic: Molecular Dynamics Simulation

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ConfRank: Improving GFN-FF Conformer Ranking with Pairwise Training.

Journal of chemical information and modeling Nov 20, 2024
Conformer ranking is a crucial task for drug discovery, with methods for generating conformers often based on molecular (meta)dynamics or sophisticated sampling techniques. These methods are constrained by the underlying force computation regarding r...
Molecular Conformation Drug Discovery Molecular Dynamics Simulation Machine Learning
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Deciphering Cas9 specificity: Role of domain dynamics and RNA:DNA hybrid interactions revealed through machine learning and accelerated molecular simulations.

International journal of biological macromolecules Nov 19, 2024
CRISPR/Cas9 technology is widely used for gene editing, but off-targeting still remains a major concern in therapeutic applications. Although Cas9 variants with better mismatch discrimination have been developed, they have significantly lower rates o...
CRISPR-Associated Protein 9 Bacterial Proteins RNA Francisella DNA Protein Domains Substrate Specificity Machine Learning CRISPR-Cas Systems Molecular Dynamics Simulation
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Emerging Frontiers in Conformational Exploration of Disordered Proteins: Integrating Autoencoder and Molecular Simulations.

ACS chemical neuroscience Nov 18, 2024
Intrinsically disordered proteins (IDPs) are closely associated with a number of neurodegenerative diseases, such as Alzheimer's disease and Parkinson's disease. Due to the highly dynamic nature of IDPs, their structural determination and conformatio...
Humans Machine Learning Molecular Dynamics Simulation Intrinsically Disordered Proteins Protein Conformation
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Estimating AChE inhibitors from MCE database by machine learning and atomistic calculations.

Journal of molecular graphics & modelling Nov 14, 2024
Acetylcholinesterase (AChE) is one of the most successful targets for the treatment of Alzheimer's disease (AD). Inhibition of AChE can result in preventing AD. In this context, the machine-learning (ML) model, molecular docking, and molecular dynami...
Molecular Docking Simulation Protein Binding Ligands Acetylcholinesterase Molecular Dynamics Simulation Binding Sites Humans Cholinesterase Inhibitors Machine Learning Databases, Chemical
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Investigating Ligand-Mediated Conformational Dynamics of Pre-miR21: A Machine-Learning-Aided Enhanced Sampling Study.

Journal of chemical information and modeling Nov 11, 2024
MicroRNAs (miRs) are short, noncoding RNA strands that regulate the activity of mRNAs by affecting the repression of protein translation, and their dysregulation has been implicated in several pathologies. miR21 in particular has been implicated in t...
RNA Precursors Ribonuclease III Ligands Peptides, Cyclic Nucleic Acid Conformation MicroRNAs Humans Molecular Dynamics Simulation Machine Learning
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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-...
Machine Learning Proteins Molecular Dynamics Simulation Neural Networks, Computer Thermodynamics
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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 (...
Aspartic Acid Endopeptidases Quantitative Structure-Activity Relationship Protons Molecular Dynamics Simulation Drug Design Hydrogen Bonding Amyloid Precursor Protein Secretases 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...
Molecular Dynamics Simulation Quantitative Structure-Activity Relationship Small Molecule Libraries Protein Binding Interleukin-1beta Receptors, Interleukin-1 Type I Machine Learning Molecular Docking Simulation Humans
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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...
Machine Learning Intrinsically Disordered Proteins Protein Conformation Static Electricity Proteome Molecular Dynamics Simulation
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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...
Protein Folding Protein Unfolding Nuclear Magnetic Resonance, Biomolecular Thermodynamics Proteins Density Functional Theory Quantum Theory Protein Conformation Molecular Dynamics Simulation Machine Learning Peptides Artificial Intelligence Time Factors
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