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Molecular Modeling and Bioinformatics

SHEBA  (Structural Homology by Environment-Based Alignment)


SHEBA is a new protein structure alignment procedure. The initial alignment is made by comparing a one-dimensional (1D) list of primary, secondary and tertiary structural profiles of two proteins, without explicitly considering the geometry of the structures. The alignment is then iteratively refined in the second step, in which new alignments are found by three-dimensional (3D) superposition of the structures based on the current alignment.

SHEBA can do pair-wise (one-to-one) alignment or multiple (one-to-many) alignment. It also has several different output options:

  • for pair-wise alignment: alignment statistics, corresponding sequence alignments, formatted column output, a list of aligned residue numbers, the transformation matrix, and the transformed coordinates in PDB-like format.
  • for multiple alignment: corresponding sequence alignments and multiple alignment statistics.

The original publication is: Jung, J. and Lee, B. Protein structure alignment using environmental profiles. Protein Engineering. 13: 535-43, 2000. PubMed Abstract, Full Text