M. V. Batsyn, V. A. Kalyagin, D. N. Tulyakov, “An efficient approach to the protein structure alignment problem”, Keldysh Institute preprints, 2015,091, 15 pp.

An efficient approach to the protein structure alignment problem

M. V. Batsyn, V. A. Kalyagin, D. N. Tulyakov

Abstract: The Protein Structure Alignment Problem (PSAP) consists in finding the best alignment of two proteins defined by their primary structures. In this paper we present an efficient algorithm for the PSAP. The computational results are provided for the popular Skolnick test set of 40 proteins and show that the suggested algorithm is more efficient than one of the fastest PSAP solvers — the ACF algorithm by Malod-Dognin et al. (2010).

Keywords: Protein alignment; branch-and-bound algorithm.

UDC: 519.8+519.7

Language: English