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Identification of Structural Domains in Proteins by a Graph Heuristic by Lorenz Wernisch; Marcel Hunting; Shoshana J. Wodak is a Biochemistry, Genetics and Molecular Biology article available to read on EtoBox.

What is Identification of Structural Domains in Proteins by a Graph Heuristic about?

A novel automatic procedure for identifying domains from protein atomic coordinates is presented. The procedure, termed STRUDL (STRUctural Domain Limits), does not take into account information on secondary structures and handles any number of domains made up of contiguous or non-contiguous chain segments. The core algorithm uses the Kernighan-Lin graph heuristic to partition the protein into residue sets which display minimum interactions between them. These interactions are deduced from the weighted Voronoi diagram. The generated partitions are accepted or rejected on the basis of optimized criteria, representing basic expected physical properties of structural domains. The graph heuristic approach is shown to be very effective, it approximates closely the exact solution provided by a branch and bound algorithm for a number of test proteins. In addition, the overall performance of STRUDL is assessed on a set of 787 representative proteins from the Protein Data Bank by comparison to domain definitions in the CATH protein classification. The domains assigned by STRUDL agree with the CATH assignments in at least 81% of the tested proteins. This result is comparable to that obtained

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Author

Lorenz Wernisch; Marcel Hunting; Shoshana J. Wodak

Publisher

John Wiley and Sons; Wiley (John Wiley & Sons); Wiley-Liss Inc; Wiley (ISSN 0887-3585)

Published

1999

Language

EN

Field

Biochemistry, Genetics and Molecular Biology (Life Sciences)