Search for structural similarity in proteins.
BACKGROUND
The expanding protein sequence and structure databases await methods allowing rapid similarity search. Geometric parameters-dihedral angle between two sequential peptide bond planes (V) and radius of curvature (R) as they appear in pentapeptide fragments in polypeptide chains-are proposed for use in evaluating structural similarity in proteins (VeaR). The parabolic (empirical) function expressing the radius of curvature's dependence on the V-angle in model polypeptides is altered in real proteins in a form characteristic for a particular protein. This can be used as a criterion for judging similarity.


RESULTS
A structural comparison of proteins representing a wide spectrum of structures was assessed versus sequence similarity analysis based on the genetic semihomology algorithm. The term 'consensus structure', analogous to 'consensus sequence', was introduced for the serpine family.


BACKGROUND
Semihom-sequence comparison freely available on request from J. Leluk. VeaR-structural comparison freely available on request from I. Roterman.
Leluk
Jacek
J
Institute of Biochemistry and Molecular Biology University of Wrocław, Tamka 2, Poland. lulu@bf.uni.wroc.pl
Konieczny
Leszek
L
Roterman
Irena
I
D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry; D000818:Animals; D002417:Cattle; D016384:Consensus Sequence; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010446:Peptide Fragments / Q000737:chemistry / Q000145:classification / Q000235:genetics; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000737:chemistry / Q000145:classification / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D015843:Serpins / Q000737:chemistry* / Q000145:classification* / Q000235:genetics
D000596:Amino Acids; D010446:Peptide Fragments; D011506:Proteins; D015843:Serpins