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Test Systems for a docking algorithm

Under the pages listed below you will find enough information to enable you to use each of the systems. Also given are various RMSD values that show how well it is possible to model the experimental crystal structure with a rigid body algorithm, starting from the unbound components.

Decoy sets are also provided for each system. There are 100 structures in each set. The first is the experimental crystal structure. The next 3 are close models, selected from our simulations. The remaining 96 are decoys, grouped into bins of 3 for each 1 Angstrom RMSD range from 9 upto 41. All of these have the highest surface complementarity scores for that range, again coming from our simulations (which also include an electrostatic binary filter). For clarification you may wish to look at this figure. The decoy sets are also available from each complex's own data page via the links below.

If you know of any other systems, where both the unbound components and the complex all have structures in the PDB, with resolutions of 3 Angstroms or better, please let us know.


  1. TRYPSIN (E.C.3.4.21.4) / AMYLOID BETA-PROTEIN PRECURSOR INHIBITOR DOMAIN (APPI)
  2. ALPHA-CHYMOTRYPSINOGEN (EC 3.4.21.1) / HUMAN PANCREATIC SECRETORY TRYPSIN INHIBITOR
  3. KALLIKREIN A (E.C.3.4.21.8) / BOVINE PANCREATIC TRYPSIN INHIBITOR
  4. SUBTILISIN BPN' (E.C.3.4.21.14) / STREPTOMYCES SUBTILISIN INHIBITOR

  5. EXTRACELLULAR DOMAIN OF TISSUE FACTOR / INHIBITORY FAB (5G9)
  6. HUMANIZED ANTI-LYSOZYME FV / LYSOZYME
  7. MONOCLONAL ANTIBODY FAB D44.1 / LYSOZYME
  8. ANTI-LYSOZYME ANTIBODY HYHEL-63 / LYSOZYME
  9. IGG1 FAB FRAGMENT / HORSE CYTOCHROME C

  10. YEAST CYTOCHROME C PEROXIDASE (CCP) / YEAST ISO-1-CYTOCHROME C
  11. BARNASE (G SPECIFIC ENDONUCLEASE) (E.C.3.1.27.-) / BARSTAR MUTANT (C40A,C82A)
  12. BETA-LACTAMSE / BETA LACTAMASE INHIBITOR PROTEIN
  13. RIBONUCLEASE INHIBITOR / RIBONUCLEASE A
  14. ACETYLCHOLINESTERASE (E.C. 3.1.1.7) / FASCICULIN-II
  15. V-1 NEF PROTEIN / WILD TYPE FYN SH3 DOMAIN
  16. HUMAN URACIL-DEOXYRIBONUCLEIC ACID GLYCOSYLASE / PROTEIN INHIBITOR
  17. RAS / RASGAP
  18. HPT DOMAIN / CHEY