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Bioinformatics Vol. 19 no. 1 2003
Pages 117-124
© 2003 Oxford University Press

Search for structural similarity in proteins

Jacek Leluk 1,2, Leszek Konieczny 3 and Irena Roterman 4,*

1 Institute of Biochemistry and Molecular Biology University of Wroclaw, Tamka 2, 50-137 Wroclaw, Poland
2 Interdisciplinary Centre for Mathematical and Computational Modeling (ICM), Pawiln skiego 5A, 02-106 Warsaw, Poland
3 Institute of Medical Biochemistry, Collegium Medicum, Jagiellonian University, Kopernika 7, 31-034 Krakow, Poland
4 Department of Biostatistics and Medical Informatics, Collegium Medicum, Jagiellonian University, Kopernika 17, 31-501 Krakow, Poland

Received on February 3, 2002 ; revised on May 27, 2002 and July 11, 2002 ; accepted on July 15, 2002

Motivation: 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.

Availability: Semihom—sequence comparison freely available on request from J. Leluk. VeaR—structural comparison freely available on request from I. Roterman.

Contact: lulu{at}bf.uni.wroc.pl for SEMIHOM program myroterm{at}cyf-kr.edu.pl for VeaR program.

* To whom correspondence should be addressed.


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