ArticleMolecules (Basel, Switzerland)2022
3D Conformational Generative Models for Biological Structures Using Graph Information-Embedded Relative Coordinates.
Article in Molecules (Basel, Switzerland), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed.
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- Redox-modulation of regulated cell death: implications for synergistic anticancer therapies.Naunyn-Schmiedeberg's archives of pharmacology · 2026Review
- Crosstalk between death-associated protein kinase 1-regulated mechanisms and dysfunctions in alzheimer's disease.Molecular biology reports · 2026Review
- Tunicamycin-induced endoplasmic reticulum stress triggers ZBP1-Mediated PANoptosis in macrophages and mouse spleen.Molecular biology reports · 2026Article
- 12-ethoxy-Marchantin A, a new macrocyclic bis-bibenzyl from Marchantia polymorpha L., exerts anti-aging activity through activating MAPKs-dependent Nrf2/HO-1 signaling pathways.Biogerontology · 2025Article
- Intranasal AβJournal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2025Article
- HEYL-mediated activation of LAMA3 influences radiotherapy response in esophageal cancer.Esophagus : official journal of the Japan Esophageal Society · 2025Article
- Granzyme B Promotes Proliferation, Migration and EMT Process in Gastric Cancer.Biochemical genetics · 2025Article
- DiffMC-Gen: A Dual Denoising Diffusion Model for Multi-Conditional Molecular Generation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Doxorubicin or Epirubicin Versus Liposomal Doxorubicin Therapy-Differences in Cardiotoxicity.Cardiovascular toxicology · 2025Review
- Simple and sensitive galactose monitoring based on capillary SERS sensor.Analytical and bioanalytical chemistry · 2024Article
- Review of research progress on intestinal microbiota based on metabolism and inflammation for depression.Archives of microbiology · 2024Review
- Molecular Graph Generation by Decomposition and Reassembling.ACS omega · 2023Article
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Authors and funding
5 authors.
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Abstract
Developing molecular generative models for directly generating 3D conformation has recently become a hot research area. Here, an autoencoder based generative model was proposed for molecular conformation generation. A unique feature of our method is that the graph information embedded relative coordinate (GIE-RC), satisfying translation and rotation invariance, was proposed as a novel way for encoding molecular three-dimensional structure. Compared with commonly used Cartesian coordinate and internal coordinate, GIE-RC is less sensitive on errors when decoding latent variables to 3D coordinates. By using this method, a complex 3D generation task can be turned into a graph node feature generation problem. Examples were shown that the GIE-RC based autoencoder model can be used for both ligand and peptide conformation generation. Additionally, this model was used as an efficient conformation sampling method to augment conformation data needed in the construction of neural network-based force field.
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