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

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Summary

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.

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  1. Division of Theoretical Molecular Biology, Institute for Molecular Biology, Academy of Sciences, Robert-Rössle Str. 10, 01115, Berlin, Germany

    J. Rose & F. Eisenmenger

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  1. J. Rose
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  2. F. Eisenmenger
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Rose, J., Eisenmenger, F. A fast unbiased comparison of protein structures by means of the Needleman-Wunsch algorithm. J Mol Evol 32, 340–354 (1991). https://doi.org/10.1007/BF02102193

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  • DOI: https://doi.org/10.1007/BF02102193

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