AIMC Topic: Molecular Dynamics Simulation

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A hybrid protocol for peptide development: integrating deep generative models and physics simulations for biomolecular design targeting IL23R/IL23.

International journal of biological macromolecules Jun 1, 2025
Recent advances in machine learning have revolutionized molecular design; however, a gap remains in integrating generative models with physics-based simulations to develop functional modulators, such as stable peptides, for challenging targets like t...
Humans Peptides Molecular Dynamics Simulation Receptors, Interleukin Interleukin-23 Deep Learning Protein Binding Drug Design
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Multidimensional computational strategies enhance the thermostability of alpha-galactosidase.

International journal of biological macromolecules Jun 1, 2025
Alpha-Galactosidase has significant industrial application value in food processing, animal nutrition and medical applications. Microbial-derived α-galactosidases predominate industrial implementation due to high productivity, yet their inherent ther...
alpha-Galactosidase Protein Engineering Thermodynamics Aspergillus Mutation Temperature Kinetics Molecular Dynamics Simulation Enzyme Stability
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Design and molecular mechanism investigation of ALK inhibitors based on virtual screening and structural descriptor modeling.

Journal of receptor and signal transduction research Jun 1, 2025
To address the challenges of target specificity and drug resistance in Anaplastic lymphoma kinase (ALK) inhibition, this study conducted a virtual screening of the BindingDB database, yielding 711 potential ALK inhibitors. Four QSAR models were estab...
Drug Design Quantitative Structure-Activity Relationship Anaplastic Lymphoma Kinase Humans Protein Binding Protein Kinase Inhibitors Molecular Docking Simulation 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...
Molecular Docking Simulation Protein Binding Humans Molecular Dynamics Simulation Cell Proliferation Computational Biology Female Machine Learning Proto-Oncogene Proteins c-pim-1 Uterine Cervical Neoplasms Flavanones Cyclin-Dependent Kinase 2
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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...
Protozoan Proteins Protein Kinase Inhibitors Deep Learning Protein Serine-Threonine Kinases Molecular Dynamics Simulation Antimalarials Plasmodium falciparum Humans Molecular Docking Simulation
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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...
Artificial Intelligence Proteins Models, Molecular Ubiquitin Thermodynamics Protein Folding Molecular Dynamics Simulation Protein Conformation
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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...
Parkinson Disease Molecular Dynamics Simulation Quantitative Structure-Activity Relationship Tryptophan Oxygenase Machine Learning Enzyme Inhibitors Humans Neural Networks, Computer Molecular Docking Simulation Biological Products
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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...
Protein Conformation Proteins Molecular Dynamics Simulation Thermodynamics
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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...
Molecular Dynamics Simulation Intrinsically Disordered Proteins Protein Conformation Machine Learning Protein Binding
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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 Machine Learning Hepatitis B virus Capsid Proteins Protein Conformation Molecular Dynamics Simulation Capsid Virus Assembly
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