title: Sequence-structure specificity of a knowledge based energy function at the secondary structure level.
abstract: BACKGROUND
  This paper investigates the sequence-structure specificity of a representative knowledge based energy function by applying it to threading at the level of secondary structures of proteins. Assessing the strengths and weaknesses of an energy function at this fundamental level provides more detailed and insightful information than at the tertiary structure level and the results obtained can be useful in tertiary level threading.
  
  
  RESULTS
  We threaded each of the 293 non-redundant proteins onto the secondary structures contained in its respective native protein (host template). We also used 68 pairs of proteins with similar folds and low sequence identity. For each pair, we threaded the sequence of one protein onto the secondary structures of the other protein. The discerning power of the total energy function and its one-body, pairwise, and mutation components is studied. We then applied our energy function to a recent study which demonstrated how a designed 11-amino acid sequence can replace distinct segments (one segment is an alpha-helix, the other is a beta-sheet) of a protein without changing its fold. We conducted random mutations of the designed sequence to determine the patterns for favorable mutations. We also studied the sequence-structure specificity at the boundaries of a secondary structure. Finally, we demonstrated how to speed up tertiary level threading by filtering out alignments found to be energetically unfavorable during the secondary structure threading.
  
  
  BACKGROUND
  The program is available on request from the authors.
  
  
  BACKGROUND
  xud@ornl.gov
authors.affiliation: Computational Biosciences Section, Life Sciences Division Center for Engineering Science Advanced Research, Computer Science and Mathematics Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6480, USA. xud@ornl.gov
authors.forename: D
authors.initials: D
authors.lastname: Xu
authors.forename: M A
authors.initials: MA
authors.lastname: Unseren
authors.forename: Y
authors.initials: Y
authors.lastname: Xu
authors.forename: E C
authors.initials: EC
authors.lastname: Uberbacher
mesh_terms: D000595:Amino Acid Sequence; D016208:Databases, Factual; D004735:Energy Transfer; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods; D012984:Software
chemical_list: D011506:Proteins