AIMC Topic: Molecular Dynamics Simulation

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Deep learning-guided design of dynamic proteins.

Science (New York, N.Y.) May 22, 2025
Deep learning has advanced the design of static protein structures, but the controlled conformational changes that are hallmarks of natural signaling proteins have remained inaccessible to de novo design. Here, we describe a general deep learning-gui...
Mutation Molecular Dynamics Simulation Deep Learning Ligands Protein Conformation Proteins Protein Engineering Allosteric Regulation
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Enhanced Exploration of Protein Conformational Space through Integration of Ultra-Coarse-Grained Models to Multiscale Workflows.

The journal of physical chemistry. B May 22, 2025
Computational techniques such as all-atom (AA) molecular dynamics (MD) simulations and coarse-grained (CG) models have been essential to study various biological problems over a wide range of scales. While AA simulations provide detailed insights, th...
Machine Learning Proteins Molecular Dynamics Simulation Protein Conformation
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CrypTothML: An Integrated Mixed-Solvent Molecular Dynamics Simulation and Machine Learning Approach for Cryptic Site Prediction.

International journal of molecular sciences May 14, 2025
Cryptic sites, which are transient binding sites that emerge through protein conformational changes upon ligand binding, are valuable targets for drug discovery, particularly for allosteric modulators. However, identifying these sites remains challen...
Ligands Solvents Binding Sites Protein Binding Proteins Molecular Dynamics Simulation Machine Learning Drug Discovery
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High-Throughput Ligand Dissociation Kinetics Predictions Using Site Identification by Ligand Competitive Saturation.

Journal of chemical theory and computation May 13, 2025
The dissociation or off rate, , of a drug molecule has been shown to be more relevant to efficacy than affinity for selected systems, motivating the development of predictive computational methodologies. These are largely based on enhanced-sampling m...
Proteins Ligands Machine Learning Kinetics Thermodynamics Molecular Dynamics Simulation
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Modeling Enzyme Reaction and Mutation by Direct Machine Learning/Molecular Mechanics Simulations.

Journal of chemical theory and computation May 13, 2025
Accurately modeling enzyme reactions through direct machine learning/molecular mechanics simulations remains challenging in describing the electrostatic coupling between the QM and MM subsystems. In this work, we proposed a reweighting ME (mechanic e...
Machine Learning Thermodynamics Mutation Acylation Aspirin Humans Cyclooxygenase 1 Molecular Dynamics Simulation Static Electricity Cyclooxygenase 2
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AMUSET-TICA: A Tensor-Based Approach for Identifying Slow Collective Variables in Biomolecular Dynamics.

Journal of chemical theory and computation May 13, 2025
Elucidating collective variables (CVs) for biomolecular dynamics is crucial for understanding numerous biological processes. By leveraging the tensor-train data structure, a multilinear version of the AMUSE (Algorithm for Multiple Unknown Signals) al...
Amyloid Precursor Protein Secretases Molecular Dynamics Simulation Dipeptides Algorithms
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Small Molecules Targeting the Structural Dynamics of AR-V7 Partially Disordered Proteins Using Deep Ensemble Docking.

Journal of chemical theory and computation May 13, 2025
The extensive conformational dynamics of partially disordered proteins hinders the efficiency of traditional in-silico structure-based drug discovery approaches due to the challenge of screening large chemical spaces of compounds, albeit with an exce...
Humans Molecular Docking Simulation Protein Conformation Binding Sites Small Molecule Libraries Molecular Dynamics Simulation Intrinsically Disordered Proteins Receptors, Androgen
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A deep learning and molecular modeling approach to repurposing Cangrelor as a potential inhibitor of Nipah virus.

Scientific reports May 12, 2025
Deforestation, urbanization, and climate change have significantly increased the risk of zoonotic diseases. Nipah virus (NiV) of Paramyxoviridae family and Henipavirus genus is transmitted by Pteropus bats. Climate-induced changes in bat migration pa...
Drug Repositioning Models, Molecular Molecular Dynamics Simulation Alanine Nipah Virus Molecular Docking Simulation Deep Learning Antiviral Agents Henipavirus Infections RNA-Dependent RNA Polymerase Humans Adenosine Monophosphate Animals
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Discovery, Biological Evaluation and Binding Mode Investigation of Novel Butyrylcholinesterase Inhibitors Through Hybrid Virtual Screening.

Molecules (Basel, Switzerland) May 8, 2025
Butyrylcholinesterase (BChE), plays a critical role in alleviating the symptoms of Alzheimer's disease (AD) by regulating acetylcholine levels, emerging as an attractive target for AD treatment. This study employed a quantitative structure-activity r...
Protein Binding Neuroprotective Agents Molecular Dynamics Simulation Molecular Docking Simulation Drug Discovery Cholinesterase Inhibitors Quantitative Structure-Activity Relationship Butyrylcholinesterase Drug Evaluation, Preclinical Alzheimer Disease Ligands Humans Machine Learning
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Machine learning assisted in Silico discovery and optimization of small molecule inhibitors targeting the Nipah virus glycoprotein.

Scientific reports May 8, 2025
The Nipah virus (NiV), a lethal pathogen from the Paramyxoviridae family, presents a significant global health threat as a result of its high mortality rate and inter-human transmission. This investigation employed in silico methods that were assiste...
Antiviral Agents Nipah Virus Computer Simulation Humans Molecular Dynamics Simulation Molecular Docking Simulation Glycoproteins Machine Learning Small Molecule Libraries Drug Discovery Viral Proteins
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