The αBB Approach in Protein Folding
In this chapter, we address the structure prediction problem in protein folding via the αBB global optimization approach. Section 16.1 provides an introduction to the protein folding problem. Section 16.2 describes the potential energy model and two solvation models based on the area and volume accessible to the solvent. Section 16.3 discusses the concepts, the algorithmic issues and the implementation of the global optimization approach αBB as it is applied to the protein folding problem. Finally, section 16.4 presents computational studies for unsolvated and solvated pentapeptides. The material presented in this chapter is based on the work of Maranas et al. (1996), Androulakis et al. (1997a), Klepeis et al. (1998), Klepeis and Floudas (1999a), and Floudas et al. (1999b).
KeywordsDihedral Angle Hydration Free Energy Global Minimum Energy Minimum Energy Conformation Global Optimization Approach
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