AIMC Topic: Molecular Dynamics Simulation

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Deciphering the mechanism of baicalein in cervical cancer via bioinformatics, machine learning and computational simulations: PIM1 and CDK2 are key target proteins.

International journal of biological macromolecules Jun 1, 2025
Cervical cancer is one of the leading causes of death among women worldwide. Current treatments are limited by chemoresistance and chemotherapeutic agents' adverse effects, prompting the search for better therapeutic alternatives. Baicalein, a natura...
Cyclin-Dependent Kinase 2 Molecular Dynamics Simulation Flavanones Molecular Docking Simulation Protein Binding Cell Proliferation Proto-Oncogene Proteins c-pim-1 Humans Machine Learning Computational Biology Female Uterine Cervical Neoplasms
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Identification of therapeutics against PfPK6 protein of Plasmodium falciparum: Structure and Deep Learning approach.

Experimental parasitology Jun 1, 2025
The Plasmodium falciparum Protein Kinase 6 (PfPK6) is a serine/threonine protein kinase categorized under the CMGC group, displaying both cyclin-dependent kinases (CDKs) and mitogen-activated protein kinases (MAPKs) activity. Previous research has in...
Humans Protein Serine-Threonine Kinases Plasmodium falciparum Molecular Dynamics Simulation Molecular Docking Simulation Deep Learning Protein Kinase Inhibitors Antimalarials Protozoan Proteins
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Characterization of conformational flexibility in protein structures by applying artificial intelligence to molecular modeling.

Journal of structural biology Jun 1, 2025
Recent AI applications have revolutionized the modeling of structurally unresolved protein regions, thereby complementing traditional computational methods. These state-of-the-art techniques can generate numerous candidate structures, significantly e...
Proteins Thermodynamics Models, Molecular Protein Conformation Ubiquitin Protein Folding Molecular Dynamics Simulation Artificial Intelligence
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Computational screening of natural products as tryptophan 2,3-dioxygenase inhibitors: Insights from CNN-based QSAR, molecular docking, ADMET, and molecular dynamics simulations.

Computers in biology and medicine Jun 1, 2025
Parkinson's disease (PD) is characterised by a complex array of motor, psychiatric, and gastrointestinal symptoms, many of which are linked to disruptions in neuroactive metabolites. Dysregulated activity of tryptophan 2,3-dioxygenase (TDO), a key en...
Tryptophan Oxygenase Enzyme Inhibitors Quantitative Structure-Activity Relationship Biological Products Humans Parkinson Disease Neural Networks, Computer Molecular Dynamics Simulation Machine Learning Molecular Docking Simulation
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for Investigating Conformational Transitions and Environmental Interactions of Proteins.

Journal of chemical theory and computation May 27, 2025
Proteins are inherently dynamic molecules, and their conformational transitions among various states are essential for numerous biological processes, which are often modulated by their interactions with surrounding environments. Although molecular dy...
Molecular Dynamics Simulation Protein Conformation Thermodynamics Proteins
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TIDGN: A Transfer Learning Framework for Predicting Interactions of Intrinsically Disordered Proteins with High Conformational Dynamics.

Journal of chemical information and modeling May 26, 2025
Interactions between intrinsically disordered proteins (IDPs) are crucial for biological processes, such as intracellular liquid-liquid phase separation (LLPS). Experiments (e.g., NMR) and simulations used to study IDP interactions encounter a variet...
Intrinsically Disordered Proteins Protein Conformation Machine Learning Protein Binding Molecular Dynamics Simulation
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Machine Learning of Molecular Dynamics Simulations Provides Insights into the Modulation of Viral Capsid Assembly.

Journal of chemical information and modeling May 26, 2025
An effective approach in the development of novel antivirals is to target the assembly of viral capsids by using capsid assembly modulators (CAMs). CAMs targeting hepatitis B virus (HBV) have two major modes of function: they can either accelerate nu...
Protein Multimerization Capsid Proteins Capsid Protein Conformation Virus Assembly Hepatitis B virus Molecular Dynamics Simulation Machine Learning
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Deep learning-guided design of dynamic proteins.

Science (New York, N.Y.) May 22, 2025
Deep learning has advanced the design of static protein structures, but the controlled conformational changes that are hallmarks of natural signaling proteins have remained inaccessible to de novo design. Here, we describe a general deep learning-gui...
Proteins Mutation Ligands Protein Conformation Molecular Dynamics Simulation Deep Learning Protein Engineering Allosteric Regulation
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Enhanced Exploration of Protein Conformational Space through Integration of Ultra-Coarse-Grained Models to Multiscale Workflows.

The journal of physical chemistry. B May 22, 2025
Computational techniques such as all-atom (AA) molecular dynamics (MD) simulations and coarse-grained (CG) models have been essential to study various biological problems over a wide range of scales. While AA simulations provide detailed insights, th...
Machine Learning Proteins Molecular Dynamics Simulation Protein Conformation
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CrypTothML: An Integrated Mixed-Solvent Molecular Dynamics Simulation and Machine Learning Approach for Cryptic Site Prediction.

International journal of molecular sciences May 14, 2025
Cryptic sites, which are transient binding sites that emerge through protein conformational changes upon ligand binding, are valuable targets for drug discovery, particularly for allosteric modulators. However, identifying these sites remains challen...
Solvents Binding Sites Molecular Dynamics Simulation Ligands Machine Learning Protein Binding Proteins Drug Discovery
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