Modeling Protein-Glycosaminoglycan Complexes: Does the Size Matter?

ABSTRACT: Docking glycosaminoglycans (GAGs) has been challenging because of the complex nature of these long periodic linear and negatively charged polysaccharides. Although standard docking tools like Autodock3 are successful when docking GAGs up to hexameric length, they experience challenges to properly dock longer GAGs. Similar limitations concern other docking approaches typically developed for docking ligands of limited size to proteins. At the same time, most of more advanced docking approaches are challenging for a user who is inexperienced with complex in silico methodologies. In this work, we evaluate the binding energies of complexes with different lengths of GAGs using all-atom molecular dynamics simulations. Based on this analysis, we propose a new docking protocol for long GAGs

SUBMITTER: Marcisz M 

PROVIDER: S-EPMC8479808 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature