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Protein Engineering vol. 4 no. 8 pp. 877-884, 1991
© 1991 Oxford University Press

RESEARCH-ARTICLE

Defining topologigical equivalences in macromolecules

N. Subbarao and I. Haneef1

Department of Biochemistry and Molecular Biology, University of Leeds Leeds LS2 9JT, UK

1To whom correspondence should be addressed

We describe a completely automated and objective method for defining topological equivalents in macromolecules. The method is based on well established techniques for identifying topologically and topographically equivalent atoms in small molecules and has been used in structural alignment of proteins and RNA molecules, and to extract fragments of molecules (protein secondary structures and RNA and DNA double helices) from structural databases consistent with some specified template structure.

Keywords: graph theory/maximal common subgraph/model building/structure prediction/topological equivalence

Received April 24, 1991; accepted September 30, 1991.


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