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. 1985 Jan;82(2):366–370. doi: 10.1073/pnas.82.2.366

Prediction of homology and divergence in the secondary structure of polypeptides.

S Pongor 1, A A Szalay 1
PMCID: PMC397039  PMID: 9606131

Abstract

A quantitative procedure is described for the comparison of secondary structure of homologous proteins. Standard predictive methods are used to generate probability profiles from pairs of homologous amino acid sequences; correlation coefficients (R) are then computed between each pair of amino acids for alpha-helix (R alpha), extended structure (R beta), turn (R(t)), and coil (R(c)). R values are >0.2 for correctly aligned homologous sequences. Unrelated or incorrectly aligned sequences give R values near zero. Lack of correlation for a segment of otherwise well-correlated sequences is used to identify structural divergence, which is then evaluated graphically by using difference profiles. A combination of these techniques correctly predicts secondary structural differences between melittin or beta-endorphin and their respective synthetic analogs. The method is potentially useful to describe evolutionary changes in protein secondary structure as well as in the design of peptide analogs.

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Selected References

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