SEGMER is a segmental threading algorithm designed to recoginzing
substructure motifs from the Protein Data Bank (PDB) library.
It first splits target sequences into segments which consists of 2-4
consecutive or non-consecutive secondary structure elements (alpha-helix,
beta-strand). The sequence segments are then threaded through the PDB
to identify conserved substructures.
It often identifies better conserved structure motifs than
the whole-chain threading
methods, especially when there is no similar
global fold existing in the PDB.
The SEGMER program is downloadable at
the download page.
S. Wu, Y. Zhang.
Recognizing Protein Substructure Similarity Using Segmental Threading.
Structure, 2010 18: 858-867
(download the PDF file).