Journal of Molecular Evolution

, Volume 32, Issue 4, pp 340–354

A fast unbiased comparison of protein structures by means of the Needleman-Wunsch algorithm

  • J. Rose
  • F. Eisenmenger

DOI: 10.1007/BF02102193

Cite this article as:
Rose, J. & Eisenmenger, F. J Mol Evol (1991) 32: 340. doi:10.1007/BF02102193


A fast dynamic programming algorithm for the spatial superposition of protein structure without prior knowledge of an initial alignment has been developed. The program was applied to serine proteases, hemoglobins, cytochromes C, small copper-binding proteins, and lysozymes. In most cases the existing structural homology could be detected in a completely unbiased way. The results of the method presented are in general agreement with other studies. Applying our method, the different alignment results obtained by other authors for serine proteases and cytochromes C can be classified in terms of different alignment parameters such as gap penalties or cut-off length. Limitations of the method are discussed.

Key words

Unbiased comparison of three-dimensional structures of proteins Superposition Needleman Wunsch algorithm Initial alignment Iterative improvement Serine proteases Cytochromes Cooper-binding proteins Lysozymes 

Copyright information

© Springer-Verlag New York Inc. 1991

Authors and Affiliations

  • J. Rose
    • 1
  • F. Eisenmenger
    • 1
  1. 1.Division of Theoretical Molecular BiologyInstitute for Molecular Biology, Academy of SciencesBerlinGermany

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