1. The Brookhaven Protein Databank (PDB)
  2. The Cambridge Structural Database (CSD)

The Brookhaven Protein Databank (PDB)

This facility can be used to search or browse the PDB and view the three-dimensional structures of database entries.

Methods for Searching the PDB

  1. Molecules R US, which can also graphically display the results (an appropriate client-side viewer is required). User input to Molecules R US is done via a Mosaic FORM.
  2. The NRL_3D database provides a searchable link between PDB entries, PIR sequences, and literature references (Dan Jacobson, Johns Hopkins Univ.).
  3. The PDB at NIH can be searched via the NIH Gopher server.
  4. The ProLink database contains protein structure, sequence homolog, and functional pattern information (Kathleen Klose and Temple Smith, BioMolecular Engineering Research Center, Boston Univ.).
  5. The PDB at Brookhaven can be searched via the Brookhaven WWW server and Brookhaven Gopher server (current, preliminary, and on hold entries).

Methods for Browsing the PDB

  1. PDB At A Glance represents an attempt to classify the molecules available in the PDB to facilitate browsing. PDB At A Glance is interfaced to Molecules R US, enabling the three-dimensional structures of entries to be graphically displayed.
  2. SCOP (Alexey Murzin, MRC Laboratory of Molecular Biology, Cambridge) classifies the PDB by structure, and provides interfaces to Molecules R US, SwissProt 3D Image, and RasMol.
  3. "The Annotated Guide to the Brookhaven Protein Data Bank" (Laura Lynn Walsh, Beckman Institute, University of Illinois) is a list of PDB entries that have been classified by molecule name and species of origin.
  4. The PDB Select List (U. Hobohm & C. Sander, EMBL, Heidelberg) groups PDB entries by their level of sequence similarity.
  5. The Protein Science Kinemage Index (Protein Science, Cambridge Univ. Press) is a collection of PDB structures that can be viewed using the program Kinemage.
  6. PDB newsletters at Brookhaven.

The Cambridge Structural Database (CSD)

This facility can be used to search the CSD and view the three-dimensional structures of database entries. Information about the database is available via the Cambridge Crystallographic Data Centre's WWW server.

Searching via Small Molecules R US

The CSD at NIH can be searched using Small Molecules R US, but access is limited to NIH users. Small Molecules R US can be used to output "FDAT" files, to output and convert FDAT files to other commonly used formats, or to graphically display the structures of search results (an appropriate client-side viewer is required). A Mosaic FORM allows several kinds of search queries (e.g. by author, compound, entry date, etc.) to be constructed by the user.

Searching via Quest

Quest is a program developed by the Cambridge Crystallographic Data Centre (CCDC) for searching the CSD. Quest can be used interactively (graphical or non-graphical interface) or in batch. The graphical interface is capable of drawing chemical structure diagrams and three-dimensional structures of search results. Quest provides additional searching capabilities above and beyond Small Molecules R US, and is preferable for expert users. Instructions for using and accessing Quest are provided elsewhere.