AIMC Topic: 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 Allosteric Regulation Protein Tyrosine Phosphatase, Non-Receptor Type 11 Artificial Intelligence Molecular Dynamics Simulation
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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...
Ligands Neural Networks, Computer 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...
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...
Machine Learning Molecular Docking Simulation Antiviral Agents 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...
Machine Learning Molecular Docking Simulation Humans Ligands TRPV Cation Channels Molecular Dynamics Simulation
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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...
Molecular Dynamics Simulation Quantitative Structure-Activity Relationship Biological Products Dipeptidyl-Peptidase IV Inhibitors Flavonoids Humans Machine Learning Algorithms Molecular Docking Simulation
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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...
Humans Machine Learning Programmed Cell Death 1 Receptor Quantitative Structure-Activity Relationship B7-H1 Antigen Molecular Docking Simulation Molecular Dynamics Simulation Immune Checkpoint Inhibitors
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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...
Small Molecule Libraries Pharmacophore Molecular Dynamics Simulation Quorum Sensing Staphylococcus aureus Bacterial Proteins Anti-Bacterial Agents Drug Discovery Machine Learning
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Probing the molecular mechanisms of α-synuclein inhibitors unveils promising natural candidates through machine-learning QSAR, pharmacophore modeling, and molecular dynamics simulations.

Molecular diversity Jul 18, 2023
Parkinson's disease is characterized by a multifactorial nature that is linked to different pathways. Among them, the abnormal deposition and accumulation of α-synuclein fibrils is considered a neuropathological hallmark of Parkinson's disease. Sever...
alpha-Synuclein Molecular Dynamics Simulation Biological Products Parkinson Disease Quantitative Structure-Activity Relationship Pharmacophore Machine Learning Molecular Docking Simulation Humans
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Impact of E484Q and L452R Mutations on Structure and Binding Behavior of SARS-CoV-2 B.1.617.1 Using Deep Learning AlphaFold2, Molecular Docking and Dynamics Simulation.

International journal of molecular sciences Jul 17, 2023
During the outbreak of COVID-19, many SARS-CoV-2 variants presented key amino acid mutations that influenced their binding abilities with angiotensin-converting enzyme 2 (hACE2) and neutralizing antibodies. For the B.1.617 lineage, there had been fea...
Deep Learning Molecular Dynamics Simulation Protein Binding Mutation Humans SARS-CoV-2 Antibodies, Neutralizing COVID-19 Molecular Docking Simulation
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