Journal of Protein Chemistry

, Volume 11, Issue 3, pp 305–320 | Cite as

Similarity between average distance maps of structurally homologous proteins

  • Takeshi Kikuchi
Article

Abstract

A similarity between average distance maps (Kikuchiet al., 1988a)—that is, predicted contact maps of two tertiary structurally homologous proteins—is examined. Comparisons of shapes of average distance maps (we refer to this as ADM) are made by superpositions of ADMs for two homologous proteins. Also, we compare shapes of actual contact maps for the pair of proteins. We search a optimal superposition mode of each pair of maps showing that two proteins are most similar. It is concluded that two ADMs are also similar when actual tertiary structures between two proteins show similarity. A criterion for similarity of maps is also proposed. The possibility of application of this method to detect weak homology between protein structures is discussed.

Key words

Average distance map tertiary structure similarity sequence homology structure comparison 

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Copyright information

© Plenum Publishing Corporation 1992

Authors and Affiliations

  • Takeshi Kikuchi
    • 1
  1. 1.Analytics and Informatics Department, International Research LaboratoriesCiba-Geigy (Japan) Ltd.TakarazukaJapan

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