Using an alignment of fragment strings for comparing protein structures

Bioinformatics. 2007 Jan 15;23(2):e219-24. 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.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Amino Acid Sequence
  • Computer Simulation
  • Models, Chemical*
  • Models, Molecular*
  • Molecular Sequence Data
  • Peptide Fragments / chemistry*
  • Peptide Mapping / methods
  • Protein Conformation
  • Proteins / chemistry*
  • Proteins / ultrastructure*
  • Sequence Alignment / methods*
  • Sequence Analysis, Protein / methods*


  • Peptide Fragments
  • Proteins