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© IRL Press Limited

Computer program Jamsek combining statistical and stereochemical rules for the prediction of protein secondary structure

Jan Mrázek and Jaroslav Kypr *

Institute of Biophysics, Czechoslovak Academy of Sciences 612 65 Brno, Czechoslovakia

*To whom reprint requests should be sent

This article briefly describes our program Jamsek written in FORTRAN for an ICL 2950/10 computer. Jamsek combines statistical and stereochemical rules most frequently encountered in literature to predict protein secondary structure from its sequence, into a single algorithm. The composite algorithm does not work better than the best existing single algorithms of Garnier et al. (J. Mol. Biol., 120, 97-120, 1978) or Lim (J. Mol. Biol., 88, 873-894, 1974) if percentage of residues with a correctly predicted secondary structure is taken as a criterion. However, it is fairly reliable in predicting the total amount of a-helices and (3-sheets in proteins, the secondary structure of highly ordered proteins or their parts and identification of long a-helices. It surpasses the previous algorithms by providing a possibility to make a notion about confidence of the predicton of the particular secondary structure elements thanks to the simultaneous availability of four independent predictions of the secondary structure and other relevant data (hydrophobic profile and helical wheel representation). The main body of this article is devoted to a demonstration that output data of Jamsek can simply be used for the prediction of protein topological class, identification of globular proteins containing hydrophobic a-helices and, as an auxiliary means, to distinguish between protein coding and non-coding nucleotide sequences.

Received on January 12, 1988; accepted on January 12, 1988

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