AIMC Topic: Molecular Dynamics Simulation

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Ai-driven de novo design of customizable membrane permeable cyclic peptides.

Journal of computer-aided molecular design Aug 9, 2025
Cyclic peptides, prized for their remarkable bioactivity and stability, hold great promise across various fields. Yet, designing membrane-penetrating bioactive cyclic peptides via traditional methods is complex and resource-intensive. To address this...
Artificial Intelligence Drug Design Peptides, Cyclic Cell Membrane Permeability Cell-Penetrating Peptides Molecular Dynamics Simulation Amino Acid Sequence
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Prediction of aggregation in monoclonal antibodies from molecular surface curvature.

Scientific reports Aug 2, 2025
Protein aggregation is one of the key challenges in the biopharmaceutical industry as its control is crucial in achieving long-term stability and efficacy of biopharmaceuticals. Attempts have been made to develop regression models for predicting the ...
Hydrophobic and Hydrophilic Interactions Protein Aggregates Machine Learning Antibodies, Monoclonal Molecular Dynamics Simulation Protein Stability
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Uncovering active ingredients and mechanisms of Pholiota adiposa in the treatment of Alzheimer's disease based on network pharmacology and bioinformatics.

Scientific reports Jul 31, 2025
Pholiota adiposa is recognized for its health benefits, particularly in Alzheimer's disease (AD), but its molecular mechanism remains elusive. Our study employs network pharmacology and machine learning to uncover its therapeutic potential. We constr...
Drugs, Chinese Herbal Molecular Dynamics Simulation Molecular Docking Simulation Computational Biology Alzheimer Disease Network Pharmacology Humans Machine Learning
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Structure-based virtual screening, molecular docking, and MD simulation studies: An in-silico approach for identifying potential MBL inhibitors.

PloS one Jul 31, 2025
The global rise of antibiotic-resistant infections has been driven in part by the spread of bacteria producing metallo-β-lactamase (MBL), particularly New Delhi metallo-β-lactamase-1 (NDM-1). Currently, there are no clinically approved inhibitors tar...
Molecular Docking Simulation Molecular Dynamics Simulation Quantitative Structure-Activity Relationship beta-Lactamase Inhibitors Drug Evaluation, Preclinical beta-Lactamases
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Machine learning analysis of molecular dynamics properties influencing drug solubility.

Scientific reports Jul 24, 2025
Solubility is critical in drug discovery and development, as it significantly influences a medication's bioavailability and therapeutic efficacy. Understanding solubility at the early stages of drug discovery is essential for minimizing resource cons...
Molecular Dynamics Simulation Solubility Water Pharmaceutical Preparations Algorithms Drug Discovery Machine Learning
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Applications of enhanced sampling methods to biomolecular self-assembly: a review.

Journal of physics. Condensed matter : an Institute of Physics journal Jul 23, 2025
This review article discusses some common enhanced sampling methods in relation to the process of self-assembly of biomolecules. An introduction to self-assembly and its challenges is covered followed by a brief overview of the methods and analysis f...
Polymers Peptides Molecular Dynamics Simulation Proteins Nucleic Acids Machine Learning
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Navigating protein landscapes with a machine-learned transferable coarse-grained model.

Nature chemistry Jul 18, 2025
The most popular and universally predictive protein simulation models employ all-atom molecular dynamics, but they come at extreme computational cost. The development of a universal, computationally efficient coarse-grained (CG) model with similar pr...
Protein Folding Proteins Machine Learning Molecular Dynamics Simulation Protein Conformation Thermodynamics
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Consensus structure prediction of A. thaliana's MCTP4 structure using prediction tools and coarse grained simulations of transmembrane domain dynamics.

PloS one Jul 15, 2025
Multiple C2 Domains and Transmembrane region Proteins (MCTPs) in plants have been identified as important functional and structural components of plasmodesmata cytoplasmic bridges, which are vital for cell-cell communication. MCTPs are endoplasmic re...
Endoplasmic Reticulum Arabidopsis Proteins Arabidopsis Molecular Dynamics Simulation Membrane Proteins Protein Conformation Deep Learning Protein Domains
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NeuralTSNE: A Python Package for the Dimensionality Reduction of Molecular Dynamics Data Using Neural Networks.

Journal of chemical information and modeling Jul 14, 2025
Unsupervised machine learning has recently gained much attention in the field of molecular dynamics (MD). Particularly, dimensionality reduction techniques have been regularly employed to analyze large volumes of high-dimensional MD data to gain insi...
Dimensionality Reduction Software Neural Networks, Computer Molecular Dynamics Simulation
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Protein Structure-Function Relationship: A Kernel-PCA Approach for Reaction Coordinate Identification.

Journal of chemical theory and computation Jul 14, 2025
In this study, we propose a Kernel-PCA model designed to capture structure-function relationships in a protein. This model also enables the ranking of reaction coordinates according to their impact on protein properties. By leveraging machine learnin...
Principal Component Analysis Receptors, G-Protein-Coupled Machine Learning Molecular Dynamics Simulation Protein Conformation Proteins Structure-Activity Relationship
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