Steiner Trees and 3-D Macromolecular Conformation
Courtney Stanton, J. MacGregor Smith
INFORMS Journal on Computing · 2004 · Volume 16 · Issue 4
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.
Keywords
proteins, Steiner trees, minimum-energy configurations
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