Protein-ligand interactions form the basis of structure-based molecular design in drug discovery. These non-covalent interactions are crucial in identifying a potential target and designing a molecule against the target. Protein-ligand interactions can also be the difference between a hit and a potential lead.
Using Flare’s XED forcefield, protein-ligand interactions such as hydrogen bonds, π-cation, π – π stacking interactions, and hydrophobic interactions can be visualized by a single click of Contacts button, situated under the Home tab. Furthermore, the type of interactions can be selected or deselected for display through the Contacts Dialog.
Each interaction is displayed in a specific color (e.g., hydrogen bonds in green, π – π stacking interactions in purple, hydrophobic contacts in grey) which can be modified from Preferences in the File menu. Conveniently, the color of hydrogen bonds varies depending on their strength. Strong H-bonds are displayed in dark green, average H-bonds in light green and weak H-bonds in cyan.
Protein-ligand interactions can also be visualized in 2D using the Interaction Map, and the image can be copied and saved using Copy and Save buttons, respectively. The view in 2D can be rotated as required.