:: DESCRIPTION
Erebus is a web server that searches the entire Protein Data Bank for a given substructure defined by a set of atoms of interest, such as the binding scaffolds for small molecules.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Bioinformatics. 2011 May 1;27(9):1327-9. doi: 10.1093/bioinformatics/btr129. Epub 2011 Apr 1.
Rigid substructure search.
Shirvanyants D1, Alexandrova AN, Dokholyan NV.
:: DESCRIPTION
PPMs is a tool for finding common substructures of the two proteins.
PPMs-sl is a tool for finding the largest matching subsets of the protein itself
PPMs-mcsl is for finding all similar substructures from different chains of the same protein.
PPMs-sub is for searching a substructure in the entire protein structure.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
PPMs / PPMs-sl / PPMs-mcsl / PPMs-sub
:: MORE INFORMATION
:: DESCRIPTION
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.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
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.
:: DESCRIPTION
DASS (Discovery of All Significant Substructures) that first identifies all substructures in unordered data (DASSSub) in a manner that is especially efficient for modular data. In addition, DASS calculates the statistical significance of the identified substructures, for sets with at most one element of each type (DASSPset), or for sets with multiple occurrence of elements (DASSPmset).
::DEVELOPER
Dr. Maik Friedel , J.Hollunder
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
DASS: Efficient Discovery and P-Value Calculation of Substructures in Unordered Data
Jens Hollunder, Maik Friedel, Andreas Beyer, Christopher T. Workman, Thomas Wilhelm
Bioinformatics (2007), 23(1): 77-83.
