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.
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Structure. 2010 Jul 14;18(7):858-67. doi: 10.1016/j.str.2010.04.007.
Recognizing protein substructure similarity using segmental threading.
Wu S1, Zhang Y.