PDB Lite

www.pdblite.org
PDB Lite for Finding 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.
New in 2008 Proteopedia.Org is an excellent place for nonspecialists to find and visualize macromolecules. Educators and students can easily create tutorials on molecules of interest, including customized interactive 3D scenes. Want to make publication quality molecular scenes, or animated molecules for Powerpoint? See Top5.MolviZ.Org.

The sites below 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)
United Kingdom (EBI, European Bioinformatics Institute, Hinxton )

For advanced searches, see Jaime Prilusky's as a powerful yet straightforward alternative to Advanced Search at RCSB. OCA can find some things that RCSB cannot. For example, OCA has query fields for Kingdom, Gene, Disease, and Function. On the other hand, RCSB 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 functioning correctly, and 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 Other Public OCA Mirror Sites were out of date, or were not operating correctly, or both.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:

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.
Step by step help on how to save a PDB file to your disk so that you can visualize it, e.g. by opening in RasMol.