Structural Blocks Retrieval in Macromolecules: Saliency and Precision Aspects
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).
Keywordsprotein motif retrieval protein structure comparison protein secondary structure protein data bases secondary structure saliency error analysis
- 2.Camoglu, O., Kahveci, T., Singh, A.: PSI: Indexing protein structures for fast similarity search. Bioinformatics 19(1), 81–83 (2007)Google Scholar
- 3.Chionh, C.H., Huang, Z., Tan, K.L., Yao, Z.: Augmenting SSEs with structural properties for rapid protein structure comparison. In: The Third IEEE Symposium on Bioinformatics and Bioengineering, pp. 341–348. IEEE Press (2003)Google Scholar
- 5.Cantoni, V., Mattia, E.: Protein Structure Analysis through Hough Transform and Range Tree. Nuovo Cimento della Società Italiana di Fisica. C. Geophysics and Space Physics 35, 39–45 (2012)Google Scholar
- 6.Cantoni, V., Ferone, A., Ozbudak, O., Petrosino, A.: Motif Retrieval by Exhaustive Matching and Couple Co-occurrences. In: Computational Intelligence Methods for Bioinformatics and Biostatistics, Houston, Texas, USA, June 12-14 (2012)Google Scholar
- 9.Cantoni, V., Ferone, A., Ozbudak, O., Petrosino, A.: Structural Analysis of Protein Secondary Structure by GHT. In: The Int. Conf. on Pattern Recognition, Tsukuba, Japan, November 11-15, pp. 1767–1770. IEEE Computer Society (2012)Google Scholar