Small molecule docking and virtual screening of candidate compounds have become an integral part of drug discovery pipelines, complementing and streamlining experimental efforts in that regard. In this chapter, we describe specific software packages and protocols that can be used to efficiently set up a computational screening using a library of compounds and a docking program. We also discuss consensus- and clustering-based approaches that can be used to assess the results, and potentially re-rank the hits. While docking programs share many common features, they may require tailored implementation of virtual screening pipelines for specific computing platforms. Here, we primarily focus on solutions for several public domain packages that are widely used in the context of drug development.