ArticleMethods in molecular biology (Clifton, N.J.)2015
Molecular dynamics simulations of glycoproteins using CHARMM.
Article in Methods in molecular biology (Clifton, N.J.), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- Atomistic modeling of lysophospholipids from the Campylobacter jejuni lipidome.Biophysical journal · 2025Article
- Development of a Sustainable Flexible Humidity Sensor Based onSensors (Basel, Switzerland) · 2025Article
- Glycan masking in immunogen design: computational and experimental methods.Frontiers in immunology · 2025Review
- Docking and Molecular Dynamics Simulations Clarify Binding Sites for Interactions of Novel Marine Sulfated Glycans with SARS-CoV-2 Spike Glycoprotein.Molecules (Basel, Switzerland) · 2023Article
- Orientational Preferences of GPI-Anchored Ly6/uPAR Proteins.International journal of molecular sciences · 2022Article
- An Integrated Mass Spectrometry-Based Glycomics-Driven Glycoproteomics Analytical Platform to Functionally Characterize Glycosylation Inhibitors.Molecules (Basel, Switzerland) · 2022Article
- Host Cell Glycocalyx Remodeling Reveals SARS-CoV-2 Spike Protein Glycomic Binding Sites.Frontiers in molecular biosciences · 2022Article
- Development of Martini 2.2 parameters for N-glycans: a case study of the HIV-1 Env glycoprotein dynamics.Glycobiology · 2021Article
- Novel Pharmaceutical Strategy for Selective Abrogation of TSP1-Induced Vascular Dysfunction by Decoy Recombinant CD47 Soluble Receptor in Prophylaxis and Treatment Models.Biomedicines · 2021Article
- Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2.Viruses · 2021Article
- DNA Aptamers Block the Receptor Binding Domain at the Spike Protein of SARS-CoV-2.Frontiers in molecular biosciences · 2021Article
- Characterization of ELISA Antibody-Antigen Interaction using Footprinting-Mass Spectrometry and Negative Staining Transmission Electron Microscopy.Journal of the American Society for Mass Spectrometry · 2018Article
- Ginger (Zingiber officinale) phytochemicals-gingerenone-A and shogaol inhibit SaHPPK: molecular docking, molecular dynamics simulations and in vitro approaches.Annals of clinical microbiology and antimicrobials · 2018Article
- Article
- Reparameterization of Solute-Solute Interactions for Amino Acid-Sugar Systems Using Isopiestic Osmotic Pressure Molecular Dynamics Simulations.Journal of chemical theory and computation · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Molecular dynamics simulations are an effective tool to study the structure, dynamics, and thermodynamics of carbohydrates and proteins. However, the simulations of heterogeneous glycoprotein systems have been limited due to the lack of appropriate molecular force field parameters describing the linkage between the carbohydrate and the protein regions as well as the tools to prepare these systems for modeling studies. In this work we outline the recent developments in the CHARMM carbohydrate force field to treat glycoproteins and describe in detail the step-by-step procedures involved in building glycoprotein geometries using CHARMM-GUI Glycan Reader.
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