Optimal protein structure alignment using maximum cliques
成果类型：
Article
署名作者：
Strickland, DM; Barnes, E; Sokol, JS
署名单位：
Winthrop University; University System of Georgia; Georgia Institute of Technology
刊物名称：
OPERATIONS RESEARCH
ISSN/ISSBN：
0030-364X
DOI：
10.1287/opre.1040.0189
发表日期：
2005
页码：
389-402
关键词：
摘要：
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.