Using an alignment of fragment strings for comparing protein structures

Abstract

Here we describe the use of a particular structure fragment library, denoted here as KL-strings, for the 1D representation of protein structure. Using KL-strings, we develop an infrastructure for comparing protein structures with a 1D representation. This study focuses on the added value gained from such a description. We show the new local structure language adds resolution to the traditional three-state (helix, strand and coil) secondary structure description, and provides a high degree of accuracy in recognizing structural similarities when used with a pairwise alignment benchmark. The results of this study have immediate applications towards fast structure recognition, and for fold prediction and classification.