AIMC Topic: Molecular Dynamics Simulation

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Machine learning and cheminformatics-based Identification of lichen-derived compounds targeting mutant PBP4 in Staphylococcus aureus.

Molecular diversity Feb 15, 2025
Penicillin-binding protein 4 (PBP4) is essential in imparting significant β-lactam antibiotics resistance in Staphylococcus aureus (S. aureus) and the mutation R200L in PBP4 is linked to β-lactam non-susceptibility in natural strains, complicating tr...
Mutation Molecular Dynamics Simulation Cheminformatics Penicillin-Binding Proteins Lichens Machine Learning Anti-Bacterial Agents Staphylococcus aureus Molecular Docking Simulation Bacterial Proteins
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A semiempirical and machine learning approach for fragment-based structural analysis of non-hydroxamate HDAC3 inhibitors.

Biophysical chemistry Feb 15, 2025
Interest in HDAC3 inhibitors (HDAC3i) for pharmacological applications outside of cancer is growing. However, concerns regarding the possible mutagenicity of the commonly used hydroxamates (zinc-binding groups, ZBGs) are also increasing. Considering ...
Molecular Structure Histone Deacetylase Inhibitors Quantitative Structure-Activity Relationship Quantum Theory Histone Deacetylases Machine Learning Molecular Dynamics Simulation Thermodynamics Molecular Docking Simulation Humans
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Artificial Intuition and accelerating the process of antimicrobial drug discovery.

Computers in biology and medicine Feb 14, 2025
New drug development is a very challenging, expensive, and usually time-consuming process. This issue is very important with regard to antimicrobials, which are affected by the global issue of the development and spread of resistance. This framework ...
Antitubercular Agents Humans Molecular Dynamics Simulation Mycobacterium tuberculosis Artificial Intelligence Drug Discovery Anti-Infective Agents Computational Biology
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Dynamic Electronic Structure Fluctuations in the De Novo Peptide ACC-Dimer Revealed by First-Principles Theory and Machine Learning.

Journal of chemical information and modeling Feb 14, 2025
Recent studies have reported long-range charge transport in peptide- and protein-based fibers and wires, rendering this class of materials as promising charge-conducting interfaces between biological systems and electronic devices. In the complex mol...
Machine Learning Peptides Molecular Dynamics Simulation Electrons Density Functional Theory Protein Conformation Protein Multimerization
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AGDIFF: Attention-Enhanced Diffusion for Molecular Geometry Prediction.

Journal of chemical information and modeling Feb 11, 2025
Accurate prediction of molecular geometries is crucial for drug discovery and materials science. Existing fast conformer prediction algorithms often rely on approximate empirical energy functions, resulting in low accuracy. More accurate methods like...
Diffusion Molecular Conformation Molecular Dynamics Simulation Machine Learning Algorithms Drug Discovery
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Modeling Boltzmann-weighted structural ensembles of proteins using artificial intelligence-based methods.

Current opinion in structural biology Feb 8, 2025
This review highlights recent advances in AI-driven methods for generating Boltzmann-weighted structural ensembles, which are crucial for understanding biomolecular dynamics and drug discovery. With the rise of deep learning models such as AlphaFold2...
Molecular Dynamics Simulation Protein Conformation Proteins Models, Molecular Drug Discovery Artificial Intelligence Deep Learning
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Scaling Graph Neural Networks to Large Proteins.

Journal of chemical theory and computation Feb 6, 2025
Graph neural network (GNN) architectures have emerged as promising force field models, exhibiting high accuracy in predicting complex energies and forces based on atomic identities and Cartesian coordinates. To expand the applicability of GNNs, and m...
Machine Learning Thermodynamics Proteins Molecular Dynamics Simulation Graph Neural Networks Neural Networks, Computer
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Artificial intelligence using a latent diffusion model enables the generation of diverse and potent antimicrobial peptides.

Science advances Feb 5, 2025
Artificial intelligence holds great promise for the design of antimicrobial peptides (AMPs); however, current models face limitations in generating AMPs with sufficient novelty and diversity, and they are rarely applied to the generation of antifunga...
Animals Microbial Sensitivity Tests Mice Artificial Intelligence Anti-Bacterial Agents Acinetobacter baumannii Candida glabrata Antimicrobial Peptides Molecular Dynamics Simulation Diffusion Antifungal Agents
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Machine learning-based screening and molecular simulations for discovering novel PARP-1 inhibitors targeting DNA repair mechanisms for breast cancer therapy.

Molecular diversity Feb 3, 2025
Cancer remains one of the leading causes of death worldwide, with the rising incidence of breast cancer being a significant public health concern. Poly (ADP-ribose) polymerase-1 (PARP-1) has emerged as a promising therapeutic target for breast cancer...
Female Breast Neoplasms Molecular Docking Simulation Humans Machine Learning Poly (ADP-Ribose) Polymerase-1 Poly(ADP-ribose) Polymerase Inhibitors DNA Repair Antineoplastic Agents Molecular Dynamics Simulation Drug Discovery
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Optimizing Biomimetic 3D Disordered Fibrous Network Structures for Lightweight, High-Strength Materials via Deep Reinforcement Learning.

Advanced science (Weinheim, Baden-Wurttemberg, Germany) Jan 23, 2025
3D disordered fibrous network structures (3D-DFNS), such as cytoskeletons, collagen matrices, and spider webs, exhibit remarkable material efficiency, lightweight properties, and mechanical adaptability. Despite their widespread in nature, the integr...
Biomimetic Materials Silk Reinforcement Machine Learning Molecular Dynamics Simulation Animals Biomimetics Deep Learning
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