Glycosaminoglycans (GAGs) are a class of anionic linear periodic polysaccharides, which play a key role in many cell signaling related processes via interactions with their protein targets. In silico analysis and, in particular, application of molecular docking approaches to these systems still experience many challenges including the need of proper treatment of solvent, which is crucial for protein-GAG interactions. Here, we describe two methods which we developed, to include solvent in the docking studies of protein-GAG systems: the first one allows to de novo predict favorable positions of water molecules as a part of a rigid receptor to be used for further molecular docking; the second one utilizes targeted molecular dynamics in explicit solvent for molecular docking.
Keywords: Atomic probes; Electrostatics-driven interactions; Explicit solvent; Free energy calculations; Glycosaminoglycans; Molecular docking; Solvent displacement; Targeted molecular dynamics.