Structural blocks retrieval in macromolecules: Saliency and precision aspects

Abstract

A structural motif is a compact 3D block of a few secondary structural elements (SSs) - each one with an average of approximately 5 and 10 residues for sheets and helices respectively - which appears in a variety of macromolecules. Several motifs pack together and form compact, semi-independent units called domains. The domain size varies from about 25 up to 500 amino acids, with an average of approximately 100 residues. This hierarchical makeup of molecules results from the generation of new sequences from preexisting ones, in fact motifs and domains are the common material used by nature to generate new functionalities. Structural biology is concerned with the study of the structure of biological macromolecules like proteins and nucleic acids, and it is expected to give more insights in the function of the protein than its amino acid sequence. In this paper we propose and analyze a possible performance of a new approach for the detection of structural blocks in large datasets such as the Protein Data Base (PDB). © 2013 Springer-Verlag.