Coarse-grained model of glycosaminoglycans

Research output: Contribution to journalResearch articleContributedpeer-review



Glycosaminoglycans (GAGs) represent a class of anionic periodic linear polysaccharides, which mediate cell communication processes by interactions with their protein targets in the extracellular matrix. Due to their high flexibility, charged nature, periodicity, and polymeric nature, GAGs are challenging systems for computational approaches. To deal with the length challenge, coarse-grained (CG) modeling could be a promising approach. In this work, we develop AMBER-compatible CG parameters for GAGs using all-atomic (AA) molecular dynamics (MD) simulations in explicit solvent and the Boltzmann conversion approach. We compare both global and local properties of GAGs obtained in the simulations with AA and CG approaches, and we conclude that our CG model is appropriate for the MD approach of long GAG molecules at long time scales.


Original languageEnglish
Pages (from-to)114-124
Number of pages11
JournalACS: Journal of Chemical Information and Modeling
Issue number1
Publication statusPublished - 26 Jan 2015

External IDs

Scopus 84921746563



  • Computational Biology/methods, Glycosaminoglycans/chemistry, Heparin/chemistry, Hydrogen Bonding, Models, Molecular, Molecular Dynamics Simulation, Proteins/chemistry, Solvents