AIMC Topic: Molecular Dynamics Simulation

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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...
Protein Conformation Normal Distribution Principal Component Analysis Proto-Oncogene Proteins p21(ras) Mutation Deep Learning Humans Molecular Dynamics Simulation Protein Binding
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Chemical analogue based drug design for cancer treatment targeting PI3K: integrating machine learning and molecular modeling.

Molecular diversity Aug 17, 2024
Cancer is a generic term for a group of disorders defined by uncontrolled cell growth and the potential to invade or spread to other parts of the body. Gene and epigenetic alterations disrupt normal cellular control, leading to abnormal cell prolifer...
Humans Machine Learning Neoplasms Molecular Dynamics Simulation Protein Binding Ligands Models, Molecular Phosphatidylinositol 3-Kinases Protein Kinase Inhibitors Phosphoinositide-3 Kinase Inhibitors Molecular Docking Simulation Class Ib Phosphatidylinositol 3-Kinase Drug Design Antineoplastic Agents
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Identification of mycobacterial Thymidylate kinase inhibitors: a comprehensive pharmacophore, machine learning, molecular docking, and molecular dynamics simulation studies.

Molecular diversity Aug 16, 2024
Thymidylate kinase (TMK) is a pivotal enzyme in Mycobacterium tuberculosis (Mtb), crucial for phosphorylating thymidine monophosphate (dTMP) to thymidine diphosphate (dTDP), thereby playing a critical role in DNA biosynthesis. Dysregulation or inhibi...
Enzyme Inhibitors Protein Kinase Inhibitors Nucleoside-Phosphate Kinase Pharmacophore Antitubercular Agents Molecular Docking Simulation Machine Learning Molecular Dynamics Simulation Protein Binding Mycobacterium tuberculosis
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Discovery of novel ULK1 inhibitors through machine learning-guided virtual screening and biological evaluation.

Future medicinal chemistry Aug 15, 2024
Build a virtual screening model for ULK1 inhibitors based on artificial intelligence. Build machine learning and deep learning classification models and combine molecular docking and biological evaluation to screen ULK1 inhibitors from 13 million co...
Molecular Docking Simulation Humans Intracellular Signaling Peptides and Proteins Molecular Dynamics Simulation Machine Learning Drug Discovery Autophagy-Related Protein-1 Homolog Drug Evaluation, Preclinical Molecular Structure Protein Kinase Inhibitors
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Navigating the landscape of enzyme design: from molecular simulations to machine learning.

Chemical Society reviews Aug 12, 2024
Global environmental issues and sustainable development call for new technologies for fine chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the alternative to the traditional organic synthesis. However, it is c...
Machine Learning Substrate Specificity Biocatalysis Animals Protein Engineering Protein Conformation Molecular Dynamics Simulation Enzymes Humans Enzyme Activation
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Spatially Resolved Uncertainties for Machine Learning Potentials.

Journal of chemical information and modeling Aug 7, 2024
Machine learning potentials have become an essential tool for atomistic simulations, yielding results close to ab initio simulations at a fraction of computational cost. With recent improvements on the achievable accuracies, the focus has now shifted...
Water Molecular Dynamics Simulation Uncertainty Machine Learning
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Combining machine learning, molecular dynamics, and free energy analysis for (5HT)-2A receptor modulator classification.

Journal of molecular graphics & modelling Aug 5, 2024
The 5-Hydroxytryptamine (5HT)-2A receptor, a key target in psychoactive drug development, presents significant challenges in the design of selective compounds. Here, we describe the construction, evaluation and validation of two machine learning (ML)...
Molecular Dynamics Simulation Receptor, Serotonin, 5-HT2A Thermodynamics Molecular Docking Simulation Drug Discovery Protein Binding Humans Machine Learning
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Machine learning-guided multi-site combinatorial mutagenesis enhances the thermostability of pectin lyase.

International journal of biological macromolecules Aug 5, 2024
Enhancing the thermostability of enzymes is crucial for industrial applications. Methods such as directed evolution are often limited by the huge sequence space and combinatorial explosion, making it difficult to obtain optimal mutants. In recent yea...
Molecular Dynamics Simulation Enzyme Stability Mutagenesis Machine Learning Temperature Mutation Polysaccharide-Lyases Mutagenesis, Site-Directed Bacillus licheniformis Protein Engineering
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Predicting Conformational Ensembles of Intrinsically Disordered Proteins: From Molecular Dynamics to Machine Learning.

The journal of physical chemistry letters Aug 2, 2024
Intrinsically disordered proteins and regions (IDP/IDRs) are ubiquitous across all domains of life. Characterized by a lack of a stable tertiary structure, IDP/IDRs populate a diverse set of transiently formed structural states that can promiscuously...
Intrinsically Disordered Proteins Protein Conformation Humans Machine Learning Molecular Dynamics Simulation
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Combined structure-based virtual screening and machine learning approach for the identification of potential dual inhibitors of ACC and DGAT2.

International journal of biological macromolecules Jul 31, 2024
Acetyl-coenzyme A carboxylase (ACC) and diacylglycerol acyltransferase 2 (DGAT2) are recognized as potential therapeutic targets for nonalcoholic fatty liver disease (NAFLD). Inhibitors targeting ACC and DGAT2 have exhibited the capacity to reduce he...
Protein Binding Humans Molecular Dynamics Simulation Diacylglycerol O-Acyltransferase Non-alcoholic Fatty Liver Disease Machine Learning Acetyl-CoA Carboxylase Enzyme Inhibitors Drug Evaluation, Preclinical Molecular Docking Simulation Binding Sites
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