This Nature Protocols paper describes in details the series of web servers developed based on FTMap including FTSite, to predict ligand-binding sites, FTFlex, to account for side chain flexibility, FTMap/param, to parameterize additional probes, and FTDyn, for mapping ensembles of protein structures. Applications of the FTMap family of servers include determining the druggability of proteins, identifying ligand moieties that are most important for binding, finding the most bound-like conformation in ensembles of unliganded protein structures and providing input for fragment-based drug design. FTMap is more accurate than classical mapping methods such as GRID and MCSS, and it is much faster than the more-recent approaches to protein mapping based on mixed molecular dynamics.