A Polynomial-Time Algorithm for the Matching of Crossing Contact-Map Patterns

Abstract. Contact maps are a model to capture the core information in the structure of biological molecules, e.g., proteins. A contact map consists of an ordered set ¡ of elements (representing a protein’s sequence of amino acids), and a set ¢ of element pairs of ¡ , called arcs (representing amino acids which are closely neighbored in the structure). Given two contact maps £ ¡ ¤ ¢ ¥ and £ ¡¦ ¤ ¢ ¦ ¥ with §¢ § ¨ §¢ ¦ §, the CONTACT MAP PATTERN MATCHING (CMPM) problem asks whether the “pattern” £ ¡¦ ¤ ¢ ¦ ¥ “occurs” in £ ¡ ¤ ¢ ¥, i.e., informally stated, whether there is a subset of §¢ ¦ § arcs in ¢ whose arc structure coincides with ¢ ¦ . CMPM captures the biological question of finding structural motifs in protein structures. In general, CMPM is NP-hard. In this paper, we show that CMPM is solvable in © £§¢ §  §¢ ¦ § ¥ time when the pattern is  ¤  -structured, i.e., when each two arcs in the pattern are disjoint or ...

• Type: Conference
• Year: 2004
• Where: WABI
• Authors: Jens Gramm
• Keywords: Algorithms, Amino Acids, CONTACT MAP PATTERN, Contact Maps, WABI 2004