AIMC Topic: Molecular Dynamics Simulation

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Virtual screening and invitro evaluation of cyclooxygenase inhibitors from using the machine learning tool.

Journal of biomolecular structure & dynamics Oct 30, 2023
has a variety of compounds, and some of these compounds may have anti-inflammatory and antioxidant properties. In the present study, we identified the compounds in the leaf extract of through Gas Chromatography-Mass Spectrometry (GC-MS) analysis an...
Machine Learning Molecular Docking Simulation Humans Cyclooxygenase Inhibitors Hydrogen Bonding Tinospora Cyclooxygenase 2 Cyclooxygenase 1 Plant Extracts Molecular Dynamics Simulation
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Predicting 3D RNA structure from the nucleotide sequence using Euclidean neural networks.

Biophysical journal Oct 14, 2023
Fast and accurate 3D RNA structure prediction remains a major challenge in structural biology, mostly due to the size and flexibility of RNA molecules, as well as the lack of diverse experimentally determined structures of RNA molecules. Unlike DNA s...
Base Sequence Nucleic Acid Conformation Molecular Dynamics Simulation RNA Neural Networks, Computer
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Application of Machine Learning Algorithms to Metadynamics for the Elucidation of the Binding Modes and Free Energy Landscape of Drug/Target Interactions: a Case Study.

Chemistry (Weinheim an der Bergstrasse, Germany) Sep 28, 2023
In the context of drug discovery, computational methods were able to accelerate the challenging process of designing and optimizing a new drug candidate. Amongst the possible atomistic simulation approaches, metadynamics (metaD) has proven very power...
Molecular Dynamics Simulation Solvents Machine Learning Algorithms Thermodynamics
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Potent multi-target natural inhibitors against SARS-CoV-2 from medicinal plants of the Himalaya: a discovery from hybrid machine learning, chemoinformatics, and simulation assisted screening.

Journal of biomolecular structure & dynamics Sep 21, 2023
The emergence and immune evasion ability of SARS-CoV-2 Omicron strains, mainly BA.5.2 and BF.7 and other variants of concern have raised global apprehensions. With this context, the discovery of multitarget inhibitors may be proven more comprehensive...
Phytochemicals Molecular Dynamics Simulation Plants, Medicinal COVID-19 Drug Treatment Machine Learning Antiviral Agents SARS-CoV-2 Humans India Molecular Docking Simulation Virus Replication Drug Discovery Cheminformatics
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Machine learning coarse-grained potentials of protein thermodynamics.

Nature communications Sep 15, 2023
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this prob...
Ataxia Telangiectasia Mutated Proteins Physics Machine Learning Thermodynamics Molecular Dynamics Simulation
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Study on the allosteric activation mechanism of SHP2 elastic network models and neural relational inference molecular dynamics simulation.

Physical chemistry chemical physics : PCCP Sep 13, 2023
As a ubiquitous protein tyrosine phosphatase, SHP2 is involved in PD-1/PD-L1 mediated tumor immune escape and undergoes substantial conformational changes. Therefore, it is considered an ideal target for tumor intervention. However, the allosteric me...
Programmed Cell Death 1 Receptor Artificial Intelligence Allosteric Regulation Molecular Dynamics Simulation Protein Tyrosine Phosphatase, Non-Receptor Type 11
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NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics.

Journal of chemical information and modeling Sep 11, 2023
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared with traditio...
Neural Networks, Computer Ligands Machine Learning Molecular Dynamics Simulation
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Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting.

Journal of chemical information and modeling Sep 4, 2023
Recent advances in cryo-electron microscopy (cryo-EM) have enabled modeling macromolecular complexes that are essential components of the cellular machinery. The density maps derived from cryo-EM experiments are often integrated with manual, knowledg...
Molecular Dynamics Simulation Microscopy, Electron Cryoelectron Microscopy Adenylate Kinase Artificial Intelligence
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Cheminformatics and machine learning approaches for repurposing anti-viral compounds against monkeypox virus thymidylate kinase.

Molecular diversity Aug 2, 2023
One of the emerging epidemic concerns is Monkeypox disease which is spreading globally. This disease is caused by the monkeypox virus (MPXV), with an increasing global incidence with an outbreak in 2022. One of the novel targets for monkeypox disease...
Molecular Dynamics Simulation Machine Learning Nucleoside-Phosphate Kinase Molecular Docking Simulation Cheminformatics Antiviral Agents Drug Repositioning
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Discovery of novel TRPV1 modulators through machine learning-based molecular docking and molecular similarity searching.

Chemical biology & drug design Jul 25, 2023
The transient receptor potential vanilloid 1 (TRPV1) channel belongs to the transient receptor potential channel superfamily and participates in many physiological processes. TRPV1 modulators (both agonists and antagonists) can effectively inhibit pa...
Molecular Docking Simulation Molecular Dynamics Simulation Humans TRPV Cation Channels Ligands Machine Learning
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