Convenient Database links

• MMDB/NCBI
• SCOP
• HSSP
• PDBREPORT
• DSSP
• ProtMotPDB
• Blocks
  
  
• Very usuful example for parsing is worked out in TUTORIAL: "STING: Enzyme/Inhibitor Interface and Structural Waters" with Blocks DataBase!

• Link to our STINGpaint: WWW tool for sequence and MSA coloring!

• Link with 3DB Browser for complex search to be performed when PDB structure pinpointing is necessary, based only on knowledge of certain keyword, for example, or resolution value within certain range. (See more on this options below!)

• Link to GRASS, a Graphics Toolkit which aims at providing sophisticated molecular graphics capabilities to biology scientists without requiring extensive training in complicated molecular graphics software or access to expensive graphics equipment.

• Link to Noncovalent Bond Finder which displays the closest contacts to ligand or interface, reports distances, walks over water bridges.

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  Searching for the right PDB file with the 3DB Browser and displaying structure and sequence data with STING
  
  
  • STING is a WWW tool for the simultaneous display of information about macromolecular structure (in STING's Graphics Frame) and sequence (in STING's Sequence Frame). The user interested in viewing a particular PDB structure can get extensive information about the particular protein and/or DNA structure including the underlying sequence, the structural water molecules, the ligands and also information about macromolecular interfaces. STING offers a simple and easy way to map a single amino acid (or nucleotide) letter code to its position in 3D, and vice versa.
    
  • The user can either input the 4 letter PDB file code and start using STING's features, or can perform a search of the PDB based on various search parameters. To this end an effective link has been established between STING and the 3DB Browser. The essential features of this link are summarized below.
  • 1. STING uses the 3DB Browser as primary search tool for identifying the PDB file to be analyzed.
  • 2. The 3DB Browser recognizes that the search request has come from STING and acknowledges this by displaying STING's logo (bee). After a desired PDB code has been located, the 3DB Browser automatically provides the option: "STING IT": which will open STING.
  • 3. The 3DB Browser also offers, independent of STING, the option to view and analyze a PDB with STING. The STING option in this case is one of the items listed among many other packages for viewing and analyzing PDB structures.
  • 4. The 3DB Browser also offers a distinct option: "STING IT" at the end of any search.
    
    
  • Further information about the 3DB Browser and STING can be found, respectively, at:
    
    
  • http://www.pdb.bnl.gov/pdb-bin/pdbmain (main entry page)
    
  • http://www.pdb.bnl.gov/pdb-docs/3DB_Browser_help.html (help page)
    and
    
  • http://honiglab.cpmc.columbia.edu/STING (main entry page)
    
  • http://honiglab.cpmc.columbia.edu/STING/help (help page)