PDB Lite

www.pdblite.org
PDB Lite for Searching and Downloading Macromolecules

PDB Lite is designed for nonspecialists who search for atomic coordinate ("PDB") files at the Protein Data Bank on an occasional basis. It is especially targeted towards students and educators. See PDB Lite: What and Why? See also Nature of 3D Structural Data.

These sites were last tested, and these lists updated on . PDB Lite is available, updated weekly with new entries from RCSB, from:

India (Bioinformatics Centre, University of Pune)
Israel (WIS, Weizmann Institute of Science, Bioinformatics, Rehovot)
United Kingdom (EBI, European Bioinformatics Institute, Hinxton )
USA (BMERC, BioMolecular Engineering Research Center, Boston U)

For advanced searches, see Jaime Prilusky's as an alternative to Advanced Search at RCSB. OCA can find some things that SearchFields cannot. For example, OCA has query fields for Kingdom, Gene, Disease, and Function. On the other hand, SearchFields can find some things more easily than OCA. For example it can limit searches to entries that contain coordinates for RNA but neither protein nor DNA, and it can find "phospholipase C" while OCA ignores the "C".

The above PDB Lite sites were keeping their databases up to date with new releases when checked on . Other Public OCA Mirror Sites were out of date, or were not operating correctly, or both.

The RCSB PDB offers a single-slot search on its main page. However, the search results are presented in the same interface as their Advanced Search. Both PDB Lite (at the above sites that are keeping it up to date on a weekly basis) and RCSB search the same dataset. However, RCSB's single-slot search does not incorporate the key features of PDB Lite, which was designed for occasional or nonspecialist users, such as students and most educators. Such features of PDB Lite include:

Very detailed help on how to save a PDB file to your disk so that you can visualize it, e.g. by opening in RasMol or Protein Explorer. PDB Lite offers instructions specific for Windows and Macintosh.
Automatic synonym expansion ("hemoglobin" also finds "haemoglobin"; "protease" also finds "proteinase"). For example, on Sept. 20, 2007, "haemoglobin" at RCSB found 61 entries, while "hemoglobin" found 385. Either term finds both spellings at PDB Lite.
A tabular report with aligned columns including "ligand" (hetero groups) is the default, without offering a large range of options not needed by beginners. It has one-click links to the PDB file header, or viewing a molecule in Jmol.
All stages in the search process minimize the use of specialized jargon, and explain it when used. Search results omits technical information not needed by PDB Lite users, such as crystallographic properties.