Defining topological equivalences in protein structures by means of a dynamic programming algorithm
- 1 June 1993
- journal article
- research article
- Published by Oxford University Press (OUP) in Protein Engineering, Design and Selection
- Vol. 6 (4) , 373-376
- https://doi.org/10.1093/protein/6.4.373
Abstract
An automatic algorithm for defining topological equivalences in protein structures is presented. The algorithm is based on a dynamic programming technique and self-consistent scoring method. We have used it to align pairs of similar protein structures of several protein families and to identify recurrent structural domains in aspartic proteinase 2APR. Its ability to find suboptimal paths permits a thorough comparison of proteins at each level in the hierarchy of the protein structure: secondary structure, super-secondary structure, domain and entire globular structure. The algorithm has been extended to the structure alignment of ribonucleic acid and can be extended to the structure alignment of any linear polymer.Keywords
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