Structural Biology

For homology modeling, TimeLogic's Tera-BLAST and DeCypherSW algorithms are perfect for comparing new sequences to the Protein Data Bank (PDB). For sequences that do not have significant homology with existing PDB structures, DeCypherHMM can be used to compare these unknown sequences against the Superfamily database with the goal of identifying SCOP protein families.

Related Scientific Citations

Below is a short list of some recent DeCypher citations for Structural Biology. For the complete list, please visit our citations page here.

1. Selecting Folded Proteins from a Library of Secondary Structural Elements
   James J. Graziano, Wenshe Liu, Roshan Perera, Bernhard H. Geierstanger, Scott A. Lesley, and Peter G. Schultz
   J Am Chem Soc. 2008 January 9; 130(1):176–185.
2. Structural and Functional Diversity of the Microbial Kinome
   Kannan N, Taylor SS, Zhai Y, Venter JC, Manning G
   PLoS Biology, March 2007, 5(3):e17
3. A model of the acid sphingomyelinase phosphoesterase domain based on its remote structural homolog purple acid phosphatase
   Marian Seto, Marc Whitlow, Margaret A. McCarrick, Subha Srinivasan, Ying Zhu, Rene Pagila, Robert Mintzer, David Light, Anthony Johns, and Janet A. Meurer-Ogden.
   Protein Sci., Dec 2004; 13(12):3172-3186.
4. The SUPERFAMILY database in 2004: additions and improvements
   Martin Madera, Christine Vogel, Sarah K. Kummerfeld, Cyrus Chothia, and Julian Gough.
   Nucleic Acids Res., Jan 2004; 32(suppl 1):D235-D239.