论文信息 - Structural Blocks Retrieval in Macromolecules: Saliency and Precision Aspects

Structural Blocks Retrieval in Macromolecules: Saliency and Precision Aspects

A structural motifais a compact 3Dablock 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).

Virginio Cantoni | Dimo T. Dimov

[1] T. Schlick,et al. Distinct energetics and closing pathways for DNA polymerase β with 8-oxoG template and different incoming nucleotides , 2007, BMC Structural Biology.

[2] Ambuj K. Singh,et al. PSI: indexing protein structures for fast similarity search , 2003, ISMB.

[3] Kian-Lee Tan,et al. Augmenting SSEs with structural properties for rapid protein structure comparison , 2003, Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings..

[4] Josef Kittler,et al. A survey of the hough transform , 1988, Comput. Vis. Graph. Image Process..

[5] A. Giuliani,et al. A computational approach identifies two regions of Hepatitis C Virus E1 protein as interacting domains involved in viral fusion process , 2009, BMC Structural Biology.

[6] Alfredo Petrosino,et al. Protein motifs retrieval by SS terns occurrences , 2013, Pattern Recognit. Lett..

[7] Alfredo Petrosino,et al. Structural analysis of protein Secondary Structure by GHT , 2012, Proceedings of the 21st International Conference on Pattern Recognition (ICPR2012).

[8] W. Kabsch,et al. Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[9] Alfredo Petrosino,et al. Searching Structural Blocks by SS Exhaustive Matching , 2012, CIBB.

[10] Dmitrij Frishman,et al. STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins , 2004, Nucleic Acids Res..