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The αBB Approach in Peptide Docking

  • Christodoulos A. Floudas
Part of the Nonconvex Optimization and Its Applications book series (NOIA, volume 37)

Abstract

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).

Keywords

Human Leukocyte Antigen Euler Angle Translation Vector Competitive Binding Assay Protein Pocket 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer Science+Business Media Dordrecht 2000

Authors and Affiliations

  • Christodoulos A. Floudas
    • 1
  1. 1.Department of Chemical EngineeringPrinceton UniversityPrincetonUSA

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