Clique-detection models in computational biochemistry and genomics

Many important problems arising in computational biochemistry and genomics have been formulated in terms of underlying combinatorial optimization models. In particular, a number have been formulated as clique-detection models. The proposed article includes an introduction to the underlying biochemistry and genomic aspects of the problems as well as to the graph-theoretic aspects of the solution approaches. Each subsequent section describes a particular type of problem, gives an example to show how the graph model can be derived, summarizes recent progress, and discusses challenges associated with solving the associated graph-theoretic models. Clique detection models include prescribing (a) a maximal clique, (b) a maximum clique, (c) a maximum weighted clique, or (d) all maximal cliques in a graph. The particular types of biochemistry and genomics problems that can be represented by a clique detection model include integration of genome mapping data, nonoverlapping local alignments, matching and comparing molecular structures, and protein docking.