AIMC Topic: Molecular Dynamics Simulation

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Unveiling Conformational States of CDK6 Caused by Binding of Vcyclin Protein and Inhibitor by Combining Gaussian Accelerated Molecular Dynamics and Deep Learning.

Molecules (Basel, Switzerland) Jun 5, 2024
CDK6 plays a key role in the regulation of the cell cycle and is considered a crucial target for cancer therapy. In this work, conformational transitions of CDK6 were identified by using Gaussian accelerated molecular dynamics (GaMD), deep learning (...
Cyclin-Dependent Kinase 6 Thermodynamics Normal Distribution Principal Component Analysis Molecular Dynamics Simulation Protein Kinase Inhibitors Binding Sites Protein Conformation Deep Learning Protein Binding Humans
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Raman Spectra of Amino Acids and Peptides from Machine Learning Polarizabilities.

Journal of chemical information and modeling Jun 3, 2024
Raman spectroscopy is an important tool in the study of vibrational properties and composition of molecules, peptides, and even proteins. Raman spectra can be simulated based on the change of the electronic polarizability with vibrations, which can n...
Neural Networks, Computer Machine Learning Density Functional Theory Amino Acids Molecular Dynamics Simulation Peptides Spectrum Analysis, Raman
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NPEX: Never give up protein exploration with deep reinforcement learning.

Journal of molecular graphics & modelling May 25, 2024
Elucidating unknown structures of proteins, such as metastable states, is critical in designing therapeutic agents. Protein structure exploration has been performed using advanced computational methods, especially molecular dynamics and Markov chain ...
Markov Chains Proteins Monte Carlo Method Algorithms Protein Conformation Molecular Dynamics Simulation Dipeptides Deep Learning
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Impact of quantum and neuromorphic computing on biomolecular simulations: Current status and perspectives.

Current opinion in structural biology May 24, 2024
New high-performance computing architectures are becoming operative, in addition to exascale computers. Quantum computers (QC) solve optimization problems with unprecedented efficiency and speed, while neuromorphic hardware (NMH) simulates neural net...
Algorithms Machine Learning Molecular Dynamics Simulation Neural Networks, Computer Quantum Theory Software
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Accelerating reliable multiscale quantum refinement of protein-drug systems enabled by machine learning.

Nature communications May 16, 2024
Biomacromolecule structures are essential for drug development and biocatalysis. Quantum refinement (QR) methods, which employ reliable quantum mechanics (QM) methods in crystallographic refinement, showed promise in improving the structural quality ...
Machine Learning SARS-CoV-2 Molecular Dynamics Simulation Quantum Theory Antiviral Agents COVID-19 Drug Treatment Humans Coronavirus 3C Proteases
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Molecular Mechanism of Phosphorylation-Mediated Impacts on the Conformation Dynamics of GTP-Bound KRAS Probed by GaMD Trajectory-Based Deep Learning.

Molecules (Basel, Switzerland) May 15, 2024
The phosphorylation of different sites produces a significant effect on the conformational dynamics of KRAS. Gaussian accelerated molecular dynamics (GaMD) simulations were combined with deep learning (DL) to explore the molecular mechanism of the ph...
Proto-Oncogene Proteins p21(ras) Guanosine Triphosphate Protein Binding Molecular Dynamics Simulation Phosphorylation Humans Protein Conformation Principal Component Analysis Deep Learning
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Adaptive Workflows of Machine Learning Illuminate the Sequential Operation Mechanism of the TAK1's Allosteric Network.

Biochemistry May 14, 2024
Allostery is a fundamental mechanism driving biomolecular processes that holds significant therapeutic concern. Our study rigorously investigates how two distinct machine-learning algorithms uniquely classify two already close-to-active DFG-in states...
MAP Kinase Kinase Kinases Molecular Dynamics Simulation Protein Conformation Allosteric Regulation Algorithms Workflow Humans Machine Learning
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Structures, dynamics, complexes, and functions: From classic computation to artificial intelligence.

Current opinion in structural biology May 13, 2024
Computational approaches can provide highly detailed insight into the molecular recognition processes that underlie drug binding, the assembly of protein complexes, and the regulation of biological functional processes. Classical simulation methods c...
Proteins Humans Artificial Intelligence Models, Molecular Molecular Dynamics Simulation Computational Biology
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MISATO: machine learning dataset of protein-ligand complexes for structure-based drug discovery.

Nature computational science May 10, 2024
Large language models have greatly enhanced our ability to understand biology and chemistry, yet robust methods for structure-based drug discovery, quantum chemistry and structural biology are still sparse. Precise biomolecule-ligand interaction data...
Drug Discovery Proteins Molecular Dynamics Simulation Machine Learning Quantum Theory Ligands
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Identifying and characterization of novel broad-spectrum bacteriocins from the Shanxi aged vinegar microbiome: Machine learning, molecular simulation, and activity validation.

International journal of biological macromolecules May 9, 2024
Shanxi aged vinegar microbiome encodes a wide variety of bacteriocins. The aim of this study was to mine, screen and characterize novel broad-spectrum bacteriocins from the large-scale microbiome data of Shanxi aged vinegar through machine learning, ...
Molecular Dynamics Simulation Microbiota Acetic Acid Escherichia coli Staphylococcus aureus Bacteriocins Machine Learning Molecular Docking Simulation Microbial Sensitivity Tests Anti-Bacterial Agents
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