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A Protein Structural Alphabet and Its Substitution Matrix CLESUM

  • Wei-Mou Zheng
  • Xin Liu
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3680)

Abstract

By using a mixture model for the density distribution of the three pseudobond angles formed by C α atoms of four consecutive residues, the local structural states are discretized as 17 conformational letters of a protein structural alphabet. This coarse-graining procedure converts a 3D structure to a 1D code sequence. A substitution matrix between these letters is constructed based on the structural alignments of the FSSP database.

Keywords

Mixture Model Hide Markov Model Protein Data Bank Density Peak Substitution Matrix 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Wei-Mou Zheng
    • 1
  • Xin Liu
    • 2
  1. 1.Institute of Theoretical PhysicsAcademia SinicaBeijingChina
  2. 2.The Interdisciplinary Center of Theoretical StudiesAcademia SinicaBeijingChina

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