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Molecular Dynamics Simulation

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Combined Physics- and Machine-Learning-Based Method to Identify Druggable Binding Sites Using SILCS-Hotspots.

Journal of chemical information and modeling Sep 16, 2024
Identifying druggable binding sites on proteins is an important and challenging problem, particularly for cryptic, allosteric binding sites that may not be obvious from X-ray, cryo-EM, or predicted structures. The Site-Identification by Ligand Compet...
Protein Conformation Binding Sites Proteins Molecular Dynamics Simulation Ligands Drug Discovery Protein Binding Machine Learning
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Integrative residue-intuitive machine learning and MD Approach to Unveil Allosteric Site and Mechanism for β2AR.

Nature communications Sep 16, 2024
Allosteric drugs offer a new avenue for modern drug design. However, the identification of cryptic allosteric sites presents a formidable challenge. Following the allostery nature of residue-driven conformation transition, we propose a state-of-the-a...
Molecular Dynamics Simulation Humans Machine Learning Protein Conformation Allosteric Site Receptors, Adrenergic, beta-2 Drug Design Allosteric Regulation
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Exploring the Global Reaction Coordinate for Retinal Photoisomerization: A Graph Theory-Based Machine Learning Approach.

Journal of chemical information and modeling Sep 11, 2024
Unraveling the reaction pathway of photoinduced reactions poses a great challenge owing to its complexity. Recently, graph theory-based machine learning combined with nonadiabatic molecular dynamics (NAMD) has been applied to obtain the global reacti...
Machine Learning Azo Compounds Photochemical Processes Retinaldehyde Molecular Dynamics Simulation Quantum Theory Isomerism
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Utilizing Molecular Dynamics Simulations, Machine Learning, Cryo-EM, and NMR Spectroscopy to Predict and Validate Protein Dynamics.

International journal of molecular sciences Sep 8, 2024
Protein dynamics play a crucial role in biological function, encompassing motions ranging from atomic vibrations to large-scale conformational changes. Recent advancements in experimental techniques, computational methods, and artificial intelligence...
Magnetic Resonance Spectroscopy Cryoelectron Microscopy Protein Conformation Nuclear Magnetic Resonance, Biomolecular Humans Machine Learning Proteins Molecular Dynamics Simulation
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In silico assessments of the small molecular boron agents to pave the way for artificial intelligence-based boron neutron capture therapy.

European journal of medicinal chemistry Sep 6, 2024
Boron neutron capture therapy (BNCT) is a highly targeted, selective and effective technique to cure various types of cancers, with less harm to the healthy cells. In principle, BNCT treatment needs to distribute the boron (B) atoms inside the tumor ...
Molecular Structure Molecular Dynamics Simulation Ligands Small Molecule Libraries Computer Simulation Humans Boron Neoplasms Boron Compounds Artificial Intelligence Molecular Docking Simulation Boron Neutron Capture Therapy
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Investigating PCB degradation by indigenous fungal strains isolated from the transformer oil-contaminated site: degradation kinetics, Bayesian network, artificial neural networks, QSAR with DFT, molecular docking, and molecular dynamics simulation.

Environmental science and pollution research international Sep 6, 2024
The widespread prevalence of polychlorinated biphenyls (PCBs) in the environment has raised major concerns due to the associated risks to human health, wildlife, and ecological systems. Here, we investigated the degradation kinetics, Bayesian network...
Molecular Docking Simulation Bayes Theorem Soil Pollutants Neural Networks, Computer Fungi Polychlorinated Biphenyls Quantitative Structure-Activity Relationship Kinetics Molecular Dynamics Simulation Biodegradation, Environmental
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Combining network pharmacology, machine learning, molecular docking and molecular dynamic to explore the mechanism of Chufeng Qingpi decoction in treating schistosomiasis.

Frontiers in cellular and infection microbiology Sep 6, 2024
BACKGROUND: Although the Chufeng Qingpi Decoction (CQD) has demonstrated clinical effectiveness in the treatment of schistosomiasis, the precise active components and the underlying mechanisms of its therapeutic action remain elusive. To achieve a pr...
Drugs, Chinese Herbal Molecular Docking Simulation Schistosomiasis Flavanones Quercetin Protein Interaction Maps Network Pharmacology Tumor Suppressor Protein p53 Molecular Dynamics Simulation Computational Biology Kaempferols Humans Machine Learning
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A Deep Learning Approach to Uncover Voltage-Gated Ion Channels' Intermediate States.

The journal of physical chemistry. B Aug 30, 2024
Owing to recent advancements in cryo-electron microscopy, voltage-gated ion channels have gained a greater comprehension of their structural characteristics. However, a significant enigma remains unsolved for a large majority of these channels: their...
Deep Learning Ion Channel Gating Molecular Dynamics Simulation Kv1.2 Potassium Channel Protein Conformation
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From Static to Dynamic Structures: Improving Binding Affinity Prediction with Graph-Based Deep Learning.

Advanced science (Weinheim, Baden-Wurttemberg, Germany) Aug 29, 2024
Accurate prediction of protein-ligand binding affinities is an essential challenge in structure-based drug design. Despite recent advances in data-driven methods for affinity prediction, their accuracy is still limited, partially because they only ta...
Thermodynamics HSP90 Heat-Shock Proteins Molecular Dynamics Simulation Ligands Deep Learning Protein Binding Drug Design Proteins
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Conformations of KRAS4B Affected by Its Partner Binding and G12C Mutation: Insights from GaMD Trajectory-Image Transformation-Based Deep Learning.

Journal of chemical information and modeling Aug 28, 2024
Binding of partners and mutations highly affects the conformational dynamics of KRAS4B, which is of significance for deeply understanding its function. Gaussian accelerated molecular dynamics (GaMD) simulations followed by deep learning (DL) and prin...
Deep Learning Protein Binding Principal Component Analysis Mutation Molecular Dynamics Simulation Protein Conformation Humans Normal Distribution Proto-Oncogene Proteins p21(ras)
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