Steiner Trees and 3-D Macromolecular Conformation

Authors:
Courtney Stanton;J. MacGregor Smith
Affiliations:
Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095-1569, USA;Department of Mechanical and Industrial Engineering, University of Massachusetts, Amherst, Massachusetts 01003, USA
Venue:
INFORMS Journal on Computing
Year:
2004

Citing 5
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Abstract

One of the key issues in biochemistry and molecular modelling is the determination of 3-D minimum-energy configurations (MECs) for macromolecular structures such as proteins and DNA. Steiner minimal trees are seen as a useful algorithmic paradigm for modelling these structures. In this paper, we examine how Steiner minimal trees (SMTs) and the Steiner ratio value comparing minimum spanning trees (MSTs) are correlated with MEC energies in a physically meaningful manner. We conclude that the carbon and nitrogen atoms are Steiner points in the Steiner minimal tree of the proteins.