Knowledge discovery in molecular biology: Identifying structural regularities in proteins^☆

Article type: Research Article

Authors: Su, Shaobing | Cook, Diane J.^{; *; 1} | Holder, Lawrence B.

Affiliations: Department of Computer Science Engineering, University of Texas, P.O. Box 23015, Arlington, TX 76019, USA

Correspondence: [*] Corresponding author. E-mail addresses: [email protected] (S. Su), [email protected] (D.J. Cook), [email protected] (L.B. Holder).

Note: [☆] Supported by NSF grant ILI-9615272 and THECB grant 003656-045.

Note: [1] http://cygnus.uta.edu/subdue.html.

Abstract: In recent years, there has been an explosive amount of molecular biology information obtained and deposited in various databases. Identifying and interpreting interesting patterns from this massive amount of information has become an essential component in directing further molecular biology research. The goal of this research is to discover structural regularities in protein sequences by applying the SUBDUE discovery system to databases found in the Brookhaven Protein Data Bank. In this paper we discuss issues relevant to this application including data preparation and representation. We report on the results of applying SUBDUE to several classes of protein structures and discuss the potential significance of these results in the study of proteins.

Keywords: Knowledge discovery, Graph match, Molecular biology, Structural databases

DOI: 10.3233/IDA-1999-3602

Journal: Intelligent Data Analysis, vol. 3, no. 6, pp. 413-436, 1999