AIMC Topic: Molecular Dynamics Simulation

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Harnessing AlphaFold to reveal hERG channel conformational state secrets.

eLife Jul 14, 2025
To design safe, selective, and effective new therapies, there must be a deep understanding of the structure and function of the drug target. One of the most difficult problems to solve has been the resolution of discrete conformational states of tran...
Molecular Dynamics Simulation Protein Conformation ERG1 Potassium Channel Humans Molecular Docking Simulation
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Tuning antibody stability and function by rational designs of framework mutations.

mAbs Jul 13, 2025
Artificial intelligence and machine learning models have been developed to engineer antibodies for specific recognition of antigens. These approaches, however, often focus on the antibody complementarity-determining region (CDR) whilst ignoring the i...
Receptor, ErbB-2 Trastuzumab Protein Engineering Molecular Dynamics Simulation Protein Stability Complementarity Determining Regions Humans Mutation
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Machine-Learning-Driven Discovery of -Phenylbenzenesulfonamides as a Novel Chemotype for Lactate Dehydrogenase A Inhibition with Anti-Pancreatic Cancer Activity.

Journal of medicinal chemistry Jul 11, 2025
Lactate dehydrogenase A (LDHA) is a promising target for cancer therapy due to its crucial role in aerobic glycolysis. Despite extensive efforts, the structural diversity of LDHA inhibitors remains limited. Here, we utilized machine learning techniqu...
Humans Machine Learning Antineoplastic Agents Cell Line, Tumor Mice Animals Drug Discovery Enzyme Inhibitors L-Lactate Dehydrogenase Lactate Dehydrogenase 5 Structure-Activity Relationship Molecular Dynamics Simulation Sulfonamides Apoptosis Pancreatic Neoplasms
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AI based natural inhibitor targeting RPS20 for colorectal cancer treatment using integrated computational approaches.

Scientific reports Jul 10, 2025
The increasing global incidence of cancer emphasizes the vital role of machine learning algorithms and artificial intelligence (AI) in identifying novel anticancer targets and developing new drugs. Computational approaches can significantly quicken r...
Ribosomal Proteins Indoles Binding Sites Machine Learning Colorectal Neoplasms Antineoplastic Agents Molecular Dynamics Simulation Molecular Docking Simulation Humans Artificial Intelligence
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Permanent magnetic droplet-derived microrobots.

Science advances Jul 9, 2025
Microrobots hold substantial potential for precision medicine. However, challenges remain in balancing multifunctional cargo loading with efficient locomotion and in predicting behavior in complex biological environments. Here, we present permanent m...
Magnetics Molecular Dynamics Simulation Microfluidics Humans Robotics
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Predicting the Effects of Charge Mutations on the Second Osmotic Virial Coefficient for Therapeutic Antibodies via Coarse-Grained Molecular Simulations and Deep Learning Methods.

Molecular pharmaceutics Jul 7, 2025
The impact of various charge mutations on the second osmotic virial coefficient was examined for three model therapeutic monoclonal antibodies (MAbs) at representative formulation pH values by using coarse-grained (CG) molecular modeling. The wild-ty...
Hydrogen-Ion Concentration Static Electricity Osmosis Antibodies, Monoclonal Mutation Algorithms Molecular Dynamics Simulation Deep Learning
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Dynamicasome-a molecular dynamics-guided and AI-driven pathogenicity prediction catalogue for all genetic mutations.

Communications biology Jul 7, 2025
Advances in genomic medicine accelerate the identification of mutations in disease-associated genes, but the pathogenicity of many mutations remains unknown, hindering their use in diagnostics and clinical decision-making. Predictive AI models are ge...
Neural Networks, Computer Artificial Intelligence Molecular Dynamics Simulation Mixed Function Oxygenases Mutation Humans
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A computational study of cardiac glycosides from Vernonia amygdalina as PI3K inhibitors for targeting HER2 positive breast cancer.

Journal of computer-aided molecular design Jul 6, 2025
The PI3K/Akt pathway plays a crucial role in regulating a broad network of proteins involved in the proliferation of HER2-positive breast cancer. The ethyl acetate fraction of Vernonia amygdalina, which contains cardiac glycosides, has been shown to ...
Machine Learning Phosphoinositide-3 Kinase Inhibitors Cardiac Glycosides Quantitative Structure-Activity Relationship Female Phosphatidylinositol 3-Kinases Molecular Docking Simulation Humans Breast Neoplasms Protein Kinase Inhibitors Molecular Dynamics Simulation Class I Phosphatidylinositol 3-Kinases Receptor, ErbB-2
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Harnessing protein language model for structure-based discovery of highly efficient and robust PET hydrolases.

Nature communications Jul 5, 2025
Plastic waste, particularly polyethylene terephthalate (PET), presents significant environmental challenges, driving extensive research into enzymatic biodegradation. However, existing PET hydrolases (PETases) are limited by narrow sequence diversity...
Polyethylene Terephthalates Molecular Dynamics Simulation Protein Conformation Crystallography, X-Ray Hydrolases
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Combination of Molecular Dynamics Simulations and Machine Learning Reveals Structural Characteristics of Stereochemistry-Specific Interdigitation of Synthetic Monomycoloyl Glycerol Analogs.

Journal of chemical information and modeling Jul 3, 2025
Synthetic monomycoloyl glycerol (MMG) analogs possess robust immunostimulatory activity and are investigated as adjuvants for subunit vaccines in preclinical and clinical studies. These synthetic lipids consist of a glycerol moiety attached to a cory...
Thermodynamics Molecular Conformation Machine Learning Glycerol Molecular Dynamics Simulation Stereoisomerism
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