The αBB Approach in Peptide Docking

In this chapter, we discuss the peptide docking problem through the αBB deterministic global optimization framework. Section 17.1 introduces the reader to the peptide docking problem. Section 17.2 presents the various methods that have been proposed for solving the peptide docking problem. Section 17.3 defines the particular peptide docking problem between the HLA-DRB1 and virus peptides. Section 17.4 presents an outline of a novel global optimization approach for the peptide docking problem, while section 17.5 introduces the mathematical modeling and the resulting problem formulation. Section 17.6 presents the global optimization approach αBB, its algorithmic issues and its interface with the atomistic level modeling for the peptide docking problem. Finally, section 17.7 discusses the computational studies for pocket 1 of the HLA-DRB1. The material presented in this chapter is based on the work of Androulakis et al. (1997b) and Floudas et al. (1999b).