Complex sentence: Whereas many high throughput techniques to investigate protein interactions can only tell you which protein interacts with which other proteins, molecular structure can give fine details about which specific parts are interacting and what kinds of chemical bonds mediate that interaction.
Split into simpler sentences: Whereas many high throughput techniques to investigate protein interactions can only tell you which protein interacts with which other proteins. Molecular structure can give fine details about which specific parts are interacting and what kinds of chemical bonds mediate that interaction.