ArticleACS omega2025
From Apo to Ligand-Bound: Unraveling PPARγ-LBD Conformational Shifts via Advanced Molecular Dynamics.
Article in ACS omega, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
6 citing papers in PubMed.
- Molecular Dynamics of PPAR Nuclear Receptors: From Ligand Binding to Transcriptional Regulation.Cells · 2026Review
- Takeda G Protein-Coupled Receptor 5 and Peroxisome Proliferator-Activated Receptor-Gamma Activation by Pinocembrin and Pinostrobin Isolated fromInternational journal of molecular sciences · 2026Article
- The contribution of phenolic endocrine-disrupting chemicals to breast cancer risk: A comprehensive bioinformatics analysis.Scientific reports · 2026Article
- The context-dependent roles of PPAR-γ in adipocyte differentiation and obesity: a master regulator with dual functions.Frontiers in nutrition · 2026Review
- HessFit: Deriving Molecule-Specific Force Fields from Quantum Mechanical Hessians.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Multiple binding modes underlieFrontiers in bioinformatics · 2026Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) is a nuclear receptor whose ligand-induced conformational changes, primarily driven by helix 12 (H12) repositioning, regulate transcriptional activity. However, the precise mechanism remains elusive. In this study, we performed classical molecular dynamics (cMD) simulations of the PPARγ ligand binding domain (LBD) in complex with two agonists (BRL, 3EA), a partial agonist (GW0072), and an antagonist (EKP), generating 3 μs trajectories for each system. To gain deeper insights, we integrated machine learning-assisted clustering with MD simulations, revealing a favorable trend in binding free energy (Δ
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.