The topology of the protein structure of all-beta- or alpha/beta-class is a special arrangement of beta-strands within beta-sheets (and alpha-helices surrounding beta-sheets) and the order of them along the polypeptide chain. Structural motifs are a subset of strands and/or helices with widely spread topology. Structural motifs are used for classification of protein structure. Because of an increasing variety of known structures, an automatic tool for motif detection is needed. MotAn is an algorithmic detector of structural motifs in a given 3D protein structure. It detects beta-hairpins, beta-meanders, beta-helices, Greek keys, interlocks, jellyrolls, beta-alpha-beta-motifs and beta-alpha-beta-helices. MotAn was tested on selected SCOP families and shown to be more sensitive detector than the PTGL and PROMOTIF programs. MotAn is available at http://mouse.belozersky.msu.ru/motan. (C) 2014 Elsevier Inc. All rights reserved.