ArticleJournal of chemical information and modeling2023
Solvent Model Benchmark for Molecular Dynamics of Glycosaminoglycans.
Article in Journal of chemical information and modeling, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Solvent Models and Charge Scaling: Benchmarks for Molecular Dynamics of Glycosaminoglycans.The journal of physical chemistry. B · 2026Article
- Elucidating key targets and mechanisms of diethyl phthalate-induced colorectal cancer through network toxicology and molecular docking.PloS one · 2026Article
- Benchmark of Available Explicit Solvent Models in CHARMM36m to Characterize Glycosaminoglycans.The journal of physical chemistry. B · 2025Article
- Water Migration through Enzyme Tunnels Is Sensitive to the Choice of Explicit Water Model.Journal of chemical information and modeling · 2025Article
- Molecular Docking in Drug Discovery: Techniques, Applications, and Advancements.Current medicinal chemistry · 2025Review
- Decrypting Glycosaminoglycan "sulfation code" with Computational Approaches.Handbook of experimental pharmacology · 2025Review
- Comparative Assessment of Water Models in Protein-Glycan Interaction: Insights from Alchemical Free Energy Calculations and Molecular Dynamics Simulations.Journal of chemical information and modeling · 2024Article
- Developing and Benchmarking Sulfate and Sulfamate Force Field Parameters via Ab Initio Molecular Dynamics Simulations To Accurately Model Glycosaminoglycan Electrostatic Interactions.Journal of chemical information and modeling · 2024Article
- Review
- Benchmarking Water Models in Molecular Dynamics of Protein-Glycosaminoglycan Complexes.Journal of chemical information and modeling · 2024Article
- A consensus structural motif for the capsular polysaccharide ofProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Review
- Extension of the SUGRES-1P Coarse-Grained Model of Polysaccharides to Heparin.Journal of chemical theory and computation · 2023Article
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Authors and funding
2 authors.
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Abstract
In computational studies of glycosaminoglycans (GAGs), a group of anionic, periodic linear polysaccharides, so far there has been very little discussion about the role of solvent models in the molecular dynamics simulations of these molecules. Predominantly, the TIP3P water model is commonly used as one of the most popular explicit water models in general. However, there are numerous alternative explicit and implicit water models that are neglected in the computational research of GAGs. Since solvent-mediated interactions are particularly important for GAG dynamic and structural properties, it would be of great interest for the GAG community to establish the solvent model that is suited the best in terms of the quality of theoretically obtained GAG parameters and, at the same time, would be reasonably demanding in terms of computational resources required. In this study, heparin (HP) was simulated using five implicit and six explicit solvent models with the aim to find out how different solvent models influence HP's molecular descriptors in the molecular dynamics simulations. Here, we initiate the search for the most appropriate solvent representation for GAG systems and we hope to encourage other groups to contribute to this highly relevant subject.
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