Once a crystal structure of a protein of interest has been determined, the relative positions of the component atoms are known, and many important properties of the molecule can be studied. These properties include the overall shape of the protein, the arrangement of subsections such as helical (alpha helical) and approximately planar (beta sheet) regions, and the location of binding sites for small molecules referred to as ligands. The ways in which protein molecules associate with each other, including other molecules of the same kind, can also be determined. Knowledge of these properties is crucial to understanding how molecules interact, how biochemical reactions occur, and how these reactions might be inhibited.

In order to facilitate the interpretation of structural data, protein molecules can be visualized by constructing physical models. However, it is now much more common to construct an electronic model using a high-speed computer. Graphic display systems can be used to illustrate molecular shapes and to manipulate parts of a model.  Using such devices, it is easy to see how a ligand might fit into a pocket in a much larger protein molecule.

Many proteins function as enzymes or catalysts for biochemical reactions in which a ligand called a substrate is transformed into another chemical substance. Enzyme-substrate binding requires highly specific shape and electrical charge complementarity. The analogy of a key fitting a lock is often used to describe the interaction of a substrate with its binding site in an enzyme molecule.