Abstract Summary Every protein family has a set of characteristic secondary structures. However, due to individual variations, a single structure is not enough to represent the whole family. OverProt can create a secondary structure consensus, showing the general fold of the family as well as its variation. Our server provides precomputed results for all CATH superfamilies and user-defined computations, visualized by an interactive viewer, which shows the secondary structure element type, length, frequency of occurrence, spatial variability and β-connectivity. Availability and implementation OverProt Server is freely available at https://overprot.ncbr.muni.cz. Supplementary information Supplementary data are available at Bioinformatics online.