AIMC Topic: Molecular Dynamics Simulation

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When is Not Enough: Evaluating Simple Metrics for Predicting Phase Separation of Intrinsically Disordered Proteins.

The journal of physical chemistry. B Sep 5, 2025
Understanding and predicting the phase behavior of intrinsically disordered proteins (IDPs) is of significant interest due to their role in many biological processes. However, effectively characterizing phase behavior and its complex dependence on pr...
Intrinsically Disordered Proteins Phase Separation Machine Learning Molecular Dynamics Simulation
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Molecular Mechanism of Na/H Antiporting in NhaA.

Journal of chemical theory and computation Sep 2, 2025
Sodium-proton antiporter NhaA of is a paradigm to investigate the mechanistic basis of the fundamental Na/H exchange in cells. However, all existing crystal structures of NhaA are inward-facing (IF), and the putative outward-facing (OF) structures a...
Escherichia coli Proteins Protein Conformation Sodium-Hydrogen Exchangers Molecular Dynamics Simulation Sodium Escherichia coli
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From AI-Driven Sequence Generation to Molecular Simulation: A Comprehensive Framework for Antimicrobial Peptide Discovery.

Journal of chemical information and modeling Aug 29, 2025
Antimicrobial Peptides (AMPs) are a promising strategy to address bacterial resistance, yet only a limited number have advanced to clinical trials. Recent advances in deep learning provide new opportunities for AMP design. Here, we propose an integra...
Drug Discovery Deep Learning Anti-Bacterial Agents Staphylococcus aureus Molecular Dynamics Simulation Amino Acid Sequence Microbial Sensitivity Tests Escherichia coli Antimicrobial Peptides
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Basic Stability Tests of Machine Learning Potentials for Molecular Simulations in Computational Drug Discovery.

Journal of chemical information and modeling Aug 27, 2025
Neural network potentials trained on quantum-mechanical data can calculate molecular interactions with relatively high speed and accuracy. However, not all neural network potentials are suitable for molecular simulations, as they might exhibit instab...
Quantum Theory Neural Networks, Computer Drug Discovery Molecular Dynamics Simulation Machine Learning
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Harnessing artificial intelligence to identify Bufalin as a molecular glue degrader of estrogen receptor alpha.

Nature communications Aug 22, 2025
Target identification in natural products plays a critical role in the development of innovative drugs. Bufalin, a compound derived from traditional medicines, has shown promising anti-cancer activity; however, its precise molecular mechanism of acti...
Bufanolides Tamoxifen Estrogen Receptor alpha Xenograft Model Antitumor Assays Drug Resistance, Neoplasm Humans Artificial Intelligence Cell Line, Tumor Animals Protein Binding Female MCF-7 Cells Molecular Docking Simulation Breast Neoplasms Molecular Dynamics Simulation Antineoplastic Agents Mice
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Integrative Computational Approaches for TRPV1 Ion Channel Inhibitor Discovery: An Integrated Machine Learning, Drug Repurposing and Molecular Simulation Approach.

Journal of chemical information and modeling Aug 21, 2025
The transient receptor potential vanilloid 1 (TRPV1) ion channel is a key mediator of pain and inflammation, making it a crucial target for developing new analgesics. Despite progress in understanding TRPV1's role, novel modulators that effectively i...
TRPV Cation Channels Molecular Docking Simulation Molecular Dynamics Simulation Humans Drug Discovery Drug Repositioning Machine Learning
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Employing Artificial Neural Networks for Optimal Storage and Facile Sharing of Molecular Dynamics Simulation Trajectories.

Journal of chemical information and modeling Aug 18, 2025
With the remarkable stride in computing power and advances in Molecular Dynamics (MD) simulation programs, the crucial challenge of storing and sharing large biomolecular simulation data sets has emerged. By leveraging AutoEncoders, a type of artific...
Neural Networks, Computer Proteins Molecular Dynamics Simulation
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Ever-Increasing Role of Computational Tools in Solid-State Pharmaceutics: Advancing Drug Development with Enhanced Molecular Understanding and Risk Assessment.

Molecular pharmaceutics Aug 13, 2025
The field of solid-state pharmaceutics comprises a broad range of investigations into various structural aspects of pharmaceutical solids, establishing a rational structure-property correlation. These solid systems allow the tunability of the physico...
Molecular Dynamics Simulation Solubility Humans Drug Development Crystallization Risk Assessment Pharmaceutical Preparations Chemistry, Pharmaceutical
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Active Learning of Atomic Size Gas/Solid Potential Energy Surfaces via Physics Aware Models.

Journal of chemical information and modeling Aug 12, 2025
We propose an active learning (AL) framework to develop classical force fields (FFs) that accurately model the potential energy surfaces (PES) of gas/solid atomic-scale complexes. A central challenge is integrating AL with flexible, computationally e...
Machine Learning Density Functional Theory Silver Gases Monte Carlo Method Thermodynamics Molecular Dynamics Simulation Surface Properties
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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...
Peptides, Cyclic Cell Membrane Permeability Molecular Dynamics Simulation Cell-Penetrating Peptides Artificial Intelligence Amino Acid Sequence Drug Design
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