title: Using an alignment of fragment strings for comparing protein structures.
abstract: BACKGROUND
  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.
authors.affiliation: Program in Bioinformatics and Systems Biology, Burnham Institute for Medical Research, La Jolla, CA, USA. idoerg@burnham.org
authors.forename: Iddo
authors.initials: I
authors.lastname: Friedberg
authors.forename: Tim
authors.initials: T
authors.lastname: Harder
authors.forename: Rachel
authors.initials: R
authors.lastname: Kolodny
authors.forename: Einat
authors.initials: E
authors.lastname: Sitbon
authors.forename: Zhanwen
authors.initials: Z
authors.lastname: Li
authors.forename: Adam
authors.initials: A
authors.lastname: Godzik
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry*; D010449:Peptide Mapping / Q000379:methods; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*
chemical_list: D010446:Peptide Fragments; D011506:Proteins