Short structural motifs: definition, identification, and applications

Short structural motifs have been studied in the last few years as an important component in our understanding of protein structures. Traditionally, protein structure organization is defined on three levels: the primary level of the amino acids sequence, the secondary level describing local patterns within the structure, and the tertiary structure level that reflects the global conformation of the chain. The classification of secondary structure elements includes a very small number of categories. Thus, it does not seem to be rich enough to describe in full the variety of possible, short structural arrangements of the Polypeptide chain. This gives rise to another intermediate level of protein structure classification: the short structural motif. This level of classification is more specific both in structural organization and in its sequence preferences, so it is suggested that this level can serve as a better bridge between the primary level and the tertiary level of protein structure.