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WABI
2004
Springer

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

10 years 9 months ago
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 ...
Jens Gramm
Added 02 Jul 2010
Updated 02 Jul 2010
Type Conference
Year 2004
Where WABI
Authors Jens Gramm
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