Chemists working in computational chemistry and chemoinformatics use software to design virtual molecules to study their structures and how they might interact with the target proteins. 

Computers are used to help design a drug which is likely to work against a particular disease. The shape of the molecule in three dimensions can be obtained from X-ray crystallography and nmr spectroscopy and then compared to the shape of the receptor site where the molecule needs to act.

Changes can be made to the virtual molecule to improve its likely action.

These techniques of computer aided drug design help chemists discover, improve or study compounds that might become effective medicines.