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The Most Wanted Structures in the PDB

The BNL PDB Web logs from the last six months of 1998 were analyzed in order to determine which structures were the most broadly accessed. A structure was considered to be "broadly accessed" if it was frequently investigated across a spectrum of Web pages and activities, namely, saving the PDB file to disk in 3DB and PDB Lite, viewing the full coordinate set, and viewing the structure in RasMol and Chime.

A structure had to be one of the 100 most frequently accessed entries by each of these actions in order to be selected. The specific URLs corresponding to these user actions are listed below with tubulin (PDB id 1tub) as an example:

  1. Viewing the full coordinates (3DB only) http://www.pdb.bnl.gov/pdb-bin/send-pdb?id=1tub
  2. Saving to a disk (3DB only):
    http://www.pdb.bnl.gov/pdb-bin/save-pdb?id=1tub
  3. Saving to a disk (PDB Lite only):
    http://www.pdb.bnl.gov/pdb-docs/litesave.html?v1=1TUB
  4. Viewing with Chime(3DB & PDB Lite) http://www.pdb.bnl.gov/pdb-bin/ccpeek?id=1TUB
  5. Viewing with RasMol(3DB & PDB Lite) http://www.pdb.bnl.gov/pdb-bin/send-ras?id=1tub

A total of 17 PDB entries met this criteria. They are listed below in alphabetical order by id:

'1A3N','HEMOGLOBIN' Deposited: 01/22/1998
'1AG2','MAJOR PRION PROTEIN' Deposited: 03/31/1997
'1ALK','ALKALINE PHOSPHATASE (E.C.3.1.3.1)' Deposited: 03/03/1993
'1AMO','OXIDOREDUCTASE' Deposited: 06/17/1997
'1AO6','SERUM ALBUMIN' Deposited: 07/18/1997
'1AOI','HISTONE H3, HISTONE H4, HISTONE H2A, HISTONE H2B/DNA COMPLEX' 
   Deposited: 07/03/1997
'1ATN','ACTIN,DEOXYRIBONUCLEASE I (DNASE I)' Deposited: 03/08/1991
'1BL8','POTASSIUM CHANNEL PROTEIN' Deposited: 07/23/1998
'1BMF','BOVINE MITOCHONDRIAL F1-ATPASE' Deposited: 03/13/1996
'1D66','GAL4/DNA COMPLEX' Deposited: 03/06/1992
'1GC1','ENVELOPE GLYCOPROTEIN GP120, SURFACE GLYCOPROTEIN CD4,
   ANTIBODY 17B (LIGHT CHAIN), ANTIBODY 17B (HEAVY CHAIN)' Deposited: 06/15/1998
'1HHO','HEMOGLOBIN A (OXY) (ALPHA CHAIN), HEMOGLOBIN A (OXY) (BETA CHAIN)'
   Deposited: 06/10/1983
'1IR3','INSULIN RECEPTOR, PEPTIDE SUBSTRATE' Deposited: 09/22/1997
'1KZU','LIGHT HARVESTING PROTEIN B-800/850' Deposited: 08/31/96
'1OCC','CYTOCHROME C OXIDASE' Deposited: 04/18/1996
'1TUB','TUBULIN' Deposited: 09/23/1997
'2ACE','ACETYLCHOLINESTERASE' Deposited: 06/23/1996

It was decided not to rank PDB entries solely by their number of hits because that number may not always provide an accurate representation of user interest in an individual entry. An example of the problem is illustrated by Cytochrome B5, id 3b5c. This entry did not meet these selection criteria, but did have a very high hit number. Cytochrome B5 was viewed in Rasmol more than 25 times as often as it was viewed using Chime. One explanation for this discrepancy is that Cytochrome B5 is used in a Web-based RasMol tutorial by Gail Rhodes of the University of Southern Maine at http://www.usm.maine.edu/~rhodes/RasTut/index.html.

An alternative analysis, carried out for the final three months of 1998, was recently circulated by Eric Martz to the PDB discussion group and may be found at http://www.rcsb.org/pdb/lists/pdb-l/199904/msg00001.html.