AIMC Topic: Molecular Dynamics Simulation

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Integrating machine learning driven virtual screening and molecular dynamics simulations to identify potential inhibitors targeting PARP1 against prostate cancer.

Scientific reports Apr 14, 2025
Prostate cancer (PC) is one of the most common types of malignancies in men, with a noteworthy increase in newly diagnosed cases in recent years. PARP1 is a ubiquitous nuclear enzyme involved in DNA repair, nuclear transport, ribosome synthesis, and ...
Prostatic Neoplasms Molecular Dynamics Simulation Poly (ADP-Ribose) Polymerase-1 Poly(ADP-ribose) Polymerase Inhibitors Male Molecular Docking Simulation Phytochemicals Humans Machine Learning
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Enhancing the understandings on SARS-CoV-2 main protease (M) mutants from molecular dynamics and machine learning.

International journal of biological macromolecules Apr 10, 2025
While star drugs like Paxlovid have shown remarkable performance in combating SARS-CoV-2, we still face serious challenges such as viral mutants and resistance. In this study, we employ a computational framework combining molecular dynamics (MD) simu...
Humans Machine Learning Protease Inhibitors Mutation Coronavirus 3C Proteases COVID-19 Molecular Dynamics Simulation SARS-CoV-2 Drug Resistance, Viral Antiviral Agents
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LEGOLAS: A Machine Learning Method for Rapid and Accurate Predictions of Protein NMR Chemical Shifts.

Journal of chemical theory and computation Apr 10, 2025
This work introduces LEGOLAS, a fully open source TorchANI-based neural network model designed to predict NMR chemical shifts for protein backbone atoms (N, Cα, Cβ, C', HN, Hα). LEGOLAS has been designed to be fast without loss of accuracy, as our mo...
Neural Networks, Computer Machine Learning Escherichia coli Proteins Nuclear Magnetic Resonance, Biomolecular Escherichia coli Proteins Molecular Dynamics Simulation
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QuantumBind-RBFE: Accurate Relative Binding Free Energy Calculations Using Neural Network Potentials.

Journal of chemical information and modeling Apr 8, 2025
Accurate prediction of protein-ligand binding affinities is crucial in drug discovery, particularly during hit-to-lead and lead optimization phases, however, limitations in ligand force fields continue to impact prediction accuracy. In this work, we ...
Protein Binding Proteins Molecular Dynamics Simulation Quantum Theory Neural Networks, Computer Ligands Thermodynamics
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Advancing Molecular Simulations: Merging Physical Models, Experiments, and AI to Tackle Multiscale Complexity.

The journal of physical chemistry letters Apr 3, 2025
Proteins and protein complexes form adaptable networks that regulate essential biochemical pathways and define cell phenotypes through dynamic mechanisms and interactions. Advances in structural biology and molecular simulations have revealed how pro...
Protein Conformation Cryoelectron Microscopy Machine Learning Proteins Molecular Dynamics Simulation
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Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model.

Cell genomics Apr 1, 2025
Signaling pathway components are well studied, but how they mediate cell-type-specific transcription responses is an unresolved problem. Using the Hippo pathway in mouse trophoblast stem cells as a model, we show that the DNA binding of signaling eff...
Phosphoproteins Trophoblasts Enhancer Elements, Genetic Adaptor Proteins, Signal Transducing DNA-Binding Proteins Molecular Dynamics Simulation TEA Domain Transcription Factors Muscle Proteins Hippo Signaling Pathway YAP-Signaling Proteins Deep Learning Protein Binding Mice Signal Transduction Transcription Factors Protein Serine-Threonine Kinases Animals
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DeePMD-GNN: A DeePMD-kit Plugin for External Graph Neural Network Potentials.

Journal of chemical information and modeling Mar 27, 2025
Machine learning potentials (MLPs) have revolutionized molecular simulation by providing efficient and accurate models for predicting atomic interactions. MLPs continue to advance and have had profound impact in applications that include drug discove...
Graph Neural Networks Software Molecular Dynamics Simulation Neural Networks, Computer Quantum Theory
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Discovery and characterization of novel FAK inhibitors for breast cancer therapy via hybrid virtual screening, biological evaluation and molecular dynamics simulations.

Bioorganic chemistry Mar 26, 2025
Focal adhesion kinase (FAK) is a critical drug target implicated in various disease pathways, including hematological malignancies and breast cancer. Therefore, identifying FAK inhibitors with novel scaffolds could offer new opportunities for develop...
Dose-Response Relationship, Drug Drug Screening Assays, Antitumor Structure-Activity Relationship Drug Discovery Antineoplastic Agents Cell Proliferation Protein Kinase Inhibitors Focal Adhesion Kinase 1 Focal Adhesion Protein-Tyrosine Kinases Molecular Structure Humans Female Molecular Dynamics Simulation Breast Neoplasms Drug Evaluation, Preclinical Molecular Docking Simulation
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Machine Learning-Guided Screening and Molecular Docking for Proposing Naturally Derived Drug Candidates Against MERS-CoV 3CL Protease.

International journal of molecular sciences Mar 26, 2025
In this study, we utilized machine learning techniques to identify potential inhibitors of the MERS-CoV 3CL protease. Among the models evaluated, the Random Forest (RF) algorithm exhibited the highest predictive performance, achieving an accuracy of ...
Molecular Dynamics Simulation Protease Inhibitors Humans Catalytic Domain Coronavirus 3C Proteases Molecular Docking Simulation Machine Learning Middle East Respiratory Syndrome Coronavirus Drug Discovery Antiviral Agents
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Insights into phosphorylation-induced influences on conformations and inhibitor binding of CDK6 through GaMD trajectory-based deep learning.

Physical chemistry chemical physics : PCCP Mar 26, 2025
The phosphorylation of residue T177 produces a significant effect on the conformational dynamics of CDK6. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) are applied to explore the molecular mechanism of the ...
Humans Deep Learning Protein Conformation Cyclin-Dependent Kinase 6 Protein Binding Protein Kinase Inhibitors Phosphorylation Thermodynamics Molecular Dynamics Simulation
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