Beilstein J. Org. Chem.2023,19, 1933–1946, doi:10.3762/bjoc.19.144
be a potential mechanism of GAG particular sequence recognition by proteins.
Keywords: glycosaminoglycan; molecular docking; protein–glycosaminoglycan interaction specificity; RS-REMD; umbrella sampling; Introduction
Glycosaminoglycans (GAGs) are long linear periodic anionic polydisperse
RS-REMD (replica exchange with repulsive scaling), an MD-based docking method [41], to assure proper binding poses of the whole ligand and ring puckering and to be consistent with further simulations. The docked ligands cover the binding site the same way as ligands in the experimental structures
complexes obtained by RS-REMD docking were performed in AMBER20 package [42]. A TIP3P truncated octahedron water box with a distance of 20 Å from the solute to the box’s border was used to solvate complexes. Na+ counterions were used to neutralize the charge of the system. Energy minimization was performed
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Graphical Abstract
Figure 1:
Graphical representation of ligands (in licorice, hydrogen atoms not shown) used in this study. Lig...