ISSN:
1432-1432
Keywords:
Unbiased comparison of three-dimensional structures of proteins
;
Superposition
;
Needleman
;
Wunsch algorithm
;
Initial alignment
;
Iterative improvement
;
Serine proteases
;
Cytochromes
;
Cooper-binding proteins
;
Lysozymes
Source:
Springer Online Journal Archives 1860-2000
Topics:
Biology
Notes:
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.
Type of Medium:
Electronic Resource
URL:
http://dx.doi.org/10.1007/BF02102193
