Using an alignment of fragment strings for comparing protein structures

作者：Friedberg Iddo^*; Harder Tim; Kolodny Rachel; Sitbon Einat; Li Zhanwen; Godzik Adam

来源：Bioinformatics, 2007, 23(2): E219-E224.

DOI：10.1093/bioinformatics/btl310

Motivation: Most methods that are used to compare protein structures use three-dimensional (3D) structural information. At the same time, it has been shown that a 1D string representation of local protein structure retains a degree of structural information. This type of representation can be a powerful tool for protein structure comparison and classification, given the arsenal of sequence comparison tools developed by computational biology. However, in order to do so, there is a need to first understand how much information is contained in various possible 1D representations of protein structure.
Results: 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.

• 出版日期2007-1-15
• 单位河北医科大学