AutoDrug is a customizable pipeline for fragment-based drug design studies which integrates beamline systems with standard crystallography programs to build personalized workflows utilizing the highly-automated SSRL macromolecular crystallography beamlines, the SSRL sample database and a full range of crystallographic software packages on high end-computing systems. AutoDrug workflows screen protein samples soaked with small molecule fragments, selects crystals and collects diffraction data, processes data, performs molecular replacement using a known model and detects electron density likely to arise from bound fragments, all without user intervention or supervision.