Algorithmic Aspects of Protein Threading

Abstract

This chapter provides an overview of computational problems and techniques for protein threading. Protein threading is one of the most powerful approaches to protein structure prediction, where protein structure prediction is to infer three-dimensional (3-D) protein structure for a given protein sequence. Protein threading can be modeled as an optimization problem. Optimal solutions can be obtained in polynomial time using simple dynamic programming algorithms if profile type score functions are employed. However, this problem is computationally hard (NP-hard) if score functions include pairwise interaction preferences between amino acid residues. Therefore, various algorithms have been developed for finding optimal or near-optimal solutions. This chapter explains the ideas employed in these algorithms. This chapter also gives brief explanations of related problems: protein threading with constraints, comparison of RNA secondary structures and protein structure alignment.