AIMC Topic: Molecular Dynamics Simulation

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Developing a predictive QSAR model for FGFR-1 inhibitors: integrating computational and experimental validation.

Journal of computer-aided molecular design Oct 4, 2025
The traditional drug discovery process is often lengthy, costly, and characterized by a high failure rate. There is a pressing need for innovative strategies to optimize this process and improve the chances of identifying effective therapeutic candid...
Antineoplastic Agents MCF-7 Cells Molecular Dynamics Simulation Animals Molecular Docking Simulation Drug Discovery Protein Kinase Inhibitors Receptor, Fibroblast Growth Factor, Type 1 Chlorocebus aethiops HEK293 Cells Quantitative Structure-Activity Relationship Humans
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Clustering and Analyzing Ensembles of Residue Interaction Networks from Molecular Dynamics Simulations.

Journal of chemical information and modeling Oct 3, 2025
Network methods and molecular dynamics (MD) simulations have become essential tools for studying protein dynamics. However, applying network methods to MD simulations of flexible proteins is a major challenge, since the high conformational heterogene...
Algorithms Protein Conformation Cluster Analysis Proteins Molecular Dynamics Simulation
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Discovering of novel umami-enhancing peptides from Flammulina filiformis: Combining virtual screening, machine learning, molecular dynamics simulations, and sensory evaluation.

Food chemistry Sep 30, 2025
This research employed integrated machine learning and bioinformatics approaches to identify umami-enhancing peptides from Flammulina filiformis, elucidate their mechanisms of umami augmentation, and validate their efficacy through sensory evaluation...
Humans Male Peptides Molecular Docking Simulation Flavoring Agents Machine Learning Flammulina Female Sodium Glutamate Adult Molecular Dynamics Simulation Taste Fungal Proteins
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Molecular Dynamics and Neural Network Analysis Reveal Sequential Gating and Allosteric Communication in FMRFamide-Activated Sodium Channels.

Journal of chemical information and modeling Sep 29, 2025
FMRFamide-activated sodium channels (FaNaCs) represent a unique class of neuropeptide-gated ion channels within the degenerin/epithelial sodium channel (DEG/ENaC) superfamily. While cryo-electron microscopy has revealed static binding architectures, ...
Ligands Protein Conformation Ion Channel Gating Neural Networks, Computer Allosteric Regulation Molecular Dynamics Simulation FMRFamide
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CNSGT: Generative Transformer for De Novo Drug Design Targeting the Central Nervous System.

Journal of chemical information and modeling Sep 26, 2025
The design of novel central nervous system (CNS) drugs presents formidable challenges due to the restrictive nature of the blood-brain barrier, which imposes stringent physicochemical requirements. Recent advances in deep learning, particularly Trans...
Deep Learning Molecular Dynamics Simulation Central Nervous System Agents Central Nervous System Dopamine Plasma Membrane Transport Proteins Humans Molecular Docking Simulation Drug Design
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Molecular dynamics simulations of proteins: an in-depth review of computational strategies, structural insights, and their role in medicinal chemistry and drug development.

Biological cybernetics Sep 26, 2025
Molecular dynamics (MD) simulations have emerged as a powerful and extensively employed tool in biomedical research, offering insights into intricate biomolecular processes such as structural flexibility and molecular interactions, and playing a pivo...
Molecular Dynamics Simulation Chemistry, Pharmaceutical Humans Drug Development Proteins
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Integrated Machine Learning and Structure-Based Virtual Screening Identify Osimertinib as a TNIK Inhibitor for Idiopathic Pulmonary Fibrosis.

Journal of chemical information and modeling Sep 25, 2025
Traf2-and Nck-interacting kinase (TNIK) has been implicated in fibrosis-associated signaling pathways and has recently emerged as a promising therapeutic target for idiopathic pulmonary fibrosis (IPF). In this study, we employed an integrated strateg...
Molecular Dynamics Simulation Drug Evaluation, Preclinical Humans Indoles Idiopathic Pulmonary Fibrosis Aniline Compounds Machine Learning Cell Line Acrylamides Molecular Docking Simulation Protein Kinase Inhibitors Protein Serine-Threonine Kinases Pyrimidines
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Investigate the potential inhibitors of sphingosine kinase 1 (SphK1) with molecular dynamics and artificial intelligence drug design methods.

Journal of molecular modeling Sep 25, 2025
CONTEXT: Sphingosine kinase 1 (SphK1) is a sphingosine kinase that can catalyze the phosphorylation of sphingosine to generate sphingosine-1-phosphate. The J-type channel of SPHK1 plays an important role in processes such as cell signaling. Therefore...
Hydrophobic and Hydrophilic Interactions Molecular Docking Simulation Humans Enzyme Inhibitors Drug Design Artificial Intelligence Phosphotransferases (Alcohol Group Acceptor) Molecular Dynamics Simulation
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Structure based drug design and machine learning approaches for identifying natural inhibitors against the human αβIII tubulin isotype.

Scientific reports Sep 24, 2025
Microtubules (MTs) play a crucial role in mitosis and are composed of α-/β-tubulin heterodimeric subunits. In eukaryotes, eight α-tubulin and ten β-tubulin isotypes have been reported, each displaying tissue-specific expression patterns. Among them, ...
Biological Products Molecular Docking Simulation Humans Binding Sites Machine Learning Drug Design Molecular Dynamics Simulation Protein Binding Tubulin Modulators Tubulin
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Novel antimicrobial peptide HFIAP-1 mutant as a β-lactamase inhibitor against extended-spectrum β-lactamases of Escherichia coli: a comprehensive in-silico approach.

Archives of microbiology Sep 24, 2025
Extended-spectrum β-lactamases in Escherichia coli poses a significant threat for clinicians in tertiary healthcare settings, rendering treatments ineffective with newer β-lactam-β-lactamase inhibitors combinations. To overcome this, the present stud...
Escherichia coli Antimicrobial Cationic Peptides Mutation Computer Simulation Molecular Docking Simulation Microbial Sensitivity Tests Antimicrobial Peptides beta-Lactamase Inhibitors Anti-Bacterial Agents Molecular Dynamics Simulation beta-Lactamases Escherichia coli Proteins
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