A segmental threading algorithm designed to recognizing substructure motifs from the Protein Data Bank (PDB) library. SEGMER 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.
Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Center for Bioinformatics and Department of Molecular Bioscience, University of Kansas, Lawrence, KS, USA; Department of Electrical Engineering, Southwest Jiaotong University, Chengdu, China
SEGMER funding source(s)
The project is supported in part by the Alfred P. Sloan Foundation, NSF Career Award (DBI 0746198), and the National Institute of General Medical Sciences (R01GM083107, R01GM084222).