Molecular Dynamics Simulation

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 Antiviral Agents India Virus Replication Cheminformatics Humans Plants, Medicinal Machine Learning COVID-19 Drug Treatment Molecular Docking Simulation Drug Discovery SARS-CoV-2

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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...

Machine Learning Thermodynamics Physics Molecular Dynamics Simulation Ataxia Telangiectasia Mutated Proteins

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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 Machine Learning Ligands 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...

Cryoelectron Microscopy Adenylate Kinase Molecular Dynamics Simulation Microscopy, Electron 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 Docking Simulation Antiviral Agents Machine Learning Nucleoside-Phosphate Kinase Drug Repositioning Cheminformatics Molecular Dynamics Simulation

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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 Dynamics Simulation Ligands Molecular Docking Simulation Humans TRPV Cation Channels Machine Learning

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Virtual screening strategy for anti-DPP-IV natural flavonoid derivatives based on machine learning.

Journal of biomolecular structure & dynamics Jul 24, 2023

Flavonoids, especially their inhibitory effect on DPP-IV activity, have been widely recognized for their antidiabetic effects. However, the variety of natural flavonoid derivatives is very rich, and even subtle structural differences can lead to seve...

Biological Products Flavonoids Algorithms Molecular Docking Simulation Dipeptidyl-Peptidase IV Inhibitors Humans Molecular Dynamics Simulation Machine Learning Quantitative Structure-Activity Relationship

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Probing the origins of programmed death ligand-1 inhibition by implementing machine learning-assisted sequential virtual screening techniques.

Molecular diversity Jul 20, 2023

PD-L1 is a key immunotarget involved in binding to its receptor PD-1. PD-L1/PD-1 interface blocking using antibodies (or small molecules) is the central area of interest for tumor suppression in various cancers. Blocking the PD-L1/PD-1 pathway in the...

Programmed Cell Death 1 Receptor Quantitative Structure-Activity Relationship B7-H1 Antigen Molecular Dynamics Simulation Molecular Docking Simulation Immune Checkpoint Inhibitors Humans Machine Learning

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Identification of inhibitors for Agr quorum sensing system of Staphylococcus aureus by machine learning, pharmacophore modeling, and molecular dynamics approaches.

Journal of molecular modeling Jul 20, 2023

CONTEXT: Staphylococcus aureus is a highly pathogenic organism that is the most common cause of postoperative complications as well as severe infections like bacteremia and infective endocarditis. By mediating the formation of biofilms and the expres...

Anti-Bacterial Agents Drug Discovery Machine Learning Small Molecule Libraries Pharmacophore Molecular Dynamics Simulation Quorum Sensing Staphylococcus aureus Bacterial Proteins

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AI Medical Compendium Topic

Explore the latest research on artificial intelligence and machine learning in medicine.

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.

Machine learning coarse-grained potentials of protein thermodynamics.

Study on the allosteric activation mechanism of SHP2 elastic network models and neural relational inference molecular dynamics simulation.

NNP/MM: Accelerating Molecular Dynamics Simulations with Machine Learning Potentials and Molecular Mechanics.

Adaptive Ensemble Refinement of Protein Structures in High Resolution Electron Microscopy Density Maps with Radical Augmented Molecular Dynamics Flexible Fitting.

Cheminformatics and machine learning approaches for repurposing anti-viral compounds against monkeypox virus thymidylate kinase.

Discovery of novel TRPV1 modulators through machine learning-based molecular docking and molecular similarity searching.

Virtual screening strategy for anti-DPP-IV natural flavonoid derivatives based on machine learning.

Probing the origins of programmed death ligand-1 inhibition by implementing machine learning-assisted sequential virtual screening techniques.

Identification of inhibitors for Agr quorum sensing system of Staphylococcus aureus by machine learning, pharmacophore modeling, and molecular dynamics approaches.

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