QShape is a fingerprint that enables scientists to prioritize compounds for screening, focusing tests where they have the highest probability of success, and to understand the properties of new compounds. Users can search or cluster molecular libraries on the basis of 3-D shape and can find shape-based matches to molecules. The software generates its descriptor from 3-D molecular data, reading molecular information in standard MOL or SD format from a file or from the standard input. The output is sent either to a file or to the standard output for use in scripts. The program integrates with the QSearch development kit.