Optimal Protein Structure Alignment Using Maximum Cliques

Dawn M. Strickland; Earl Barnes; Joel S. Sokol

doi:10.1287/opre.1040.0189

Optimal Protein Structure Alignment Using Maximum Cliques

Dawn M. Strickland¹; Earl Barnes²; Joel S. Sokol²

¹ Department of Mathematics, Winthrop University, Rock Hill, South Carolina 29733 · ² School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332

Operations Research 2005

In biology, the protein structure alignment problem answers the question of how similar two proteins are. Proteins with strong physical similarities in their tertiary (folded) structure often have similar functions, so understanding physical similarity could be a key to developing protein-based medical treatments. One of the models for protein structure alignment is the maximum contact map overlap (CMO) model. The CMO model of protein structure alignment can be cast as a maximum clique problem on an appropriately defined graph. We exploit properties of these protein-based maximum clique problems to develop specialized preprocessing techniques and show how they can be used to more quickly solve contact map overlap instances to optimality.

DOI: 10.1287/opre.1040.0189
Volume: 53 (3)
Pages: 389-402
Language: en
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Sources: crossref