The PDBFINDER database

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 database in the current form can be downloaded by ftp as a compressed file [1900kB] or a gzipped file [1100kB], and is also distributed as part of the WHAT IF program. A convenient user interface to querying this database (and many others) is provided by Thure Etzold's SRS system. The database currently contains the following fields:

• ID
• Header
  • Date
• Compound
  • Enzyme-Code
• Source
  • Expr-Sys
• Author
• Exp-Method
  • Resolution
  • R-Factor
    • Free-R
  • N-Models
  • SF-Type
    • N-refl
    • H-min
    • H-max
    • K-min
    • K-max
    • L-min
    • L-max
• Ref-Prog
• HSSP-N-Align
• T-Frac-Helix
• T-Frac-Beta
• T-Nres-Prot
  • T-non-Std
• T-Nres-Nucl
• T-Water-Mols
• HET-Groups
  • Het-Id
  • Natom
  • Name
• Chain
  • Sec-Struc
    • Helix
      • i,i+3
      • i,i+5
    • Beta
      • B-Bridge
      • E-Beta
      • Para-Hb
      • Anti-Hb
  • Amino-Acids
    • non-Std
    • Miss-BB
    • Miss-SC
    • only-Ca
    • UNK
    • CYSS
    • Break
  • Nucl-Acids
  • Substrate
  • Water-Mols
  • Sequence