The PDB is a very information rich protein structure database. Unfortunately, the PDB people are not very good at making their data available for search engines. There are several reasons why search engines often fail on the PDB:
The PDBFINDER project is a possible solution to these problems. The PDBFINDER holds for each PDB file a structured, search-engine-friendly-formatted entry that holds the data-items most likely needed for people search for certain types of PDB entries. The PDBFINDER is not useful to search in atomic coordinates; it is meant to ad searches in the administrative records of PDB files.
Originally, we designed the PDBFINDER just for searching in PDB files. However, as all the time more people are using the PDBFINDER to aid modelling and database projects, we decided to also produce the so-called PDBFINDER2. The PDBFINDER2 also holds a lot of quality information about the PDB entries. Please only use the PDBFINDER2 if you really need that quality determination aspect because the PDBFINDER2 is five times bigger than the original PDBFINDER.
The PDBFINDER database is a database that is constructed using a PERL script from the PDB, DSSP and HSSP databases. Many of the fields contained in the PDBFINDER database are difficult to access from the original databases. Some information is retrieved from the original literature. The PDBFINDER database was constructed by Rob W.W. Hooft, Michael Scharf, Chris Sander, and Gert Vriend. Since 2000 maintenance is performed by Elmar Krieger.
If you use the PDBFINDER or PDBFINDER2 facilities we would appreciate if you were to cite
A series of PDB related databases for everyday needs.
Wouter G Touw, Coos Baakman, Jon Black, Tim AH te Beek, E Krieger, Robbie P Joosten, Gert Vriend.
Nucleic Acids Research 2015 January; 43(Database issue): D364-D368.
The PDBFINDER database: A summary of PDB, DSSP and HSSP information with added value.
R.W.W. Hooft, C. Sander and G. Vriend.,
CABIOS (1996) 12, 525-529.
(CABIOS is called Bioinformatics these days)
The PDBFinder II Database
Elmar Krieger, Rob W.W. Hooft, Sander B. Nabuurs and Gert Vriend
Rejected for publication.