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Table 1 Docking results for eight Protein Data Bank (PDB) complexes using DOVIS 2.0.

From: DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0

PDB code Receptor-ligand complex All-atom model Polar-hydrogen model
   RMSD (Å) Scorea RMSD (Å) Scorea
186L Lysozyme(L99A)/n-butylbenzene 0.59 3.33 0.80 4.03
1ABE Arabinose-binding protein/α-L-arabinose 2.64 4.58 2.33 4.08
1BR6 Ricin A chain/pteroid acid 0.62 5.40 0.75 5.27
1KIM Thymidine kinase/deoxythymidine 1.17 3.87 0.73 4.31
1RBP Retinol-binding protein/retinol 1.98 -18.88 1.54 5.92
1STP Streptavidin/biotin 0.83 5.16 0.81 5.31
3PTB Trypsin/benzamidine 0.48 3.37 0.48 3.54
4DFR Dihydrofolatereductase/methotrexate 5.06 4.59 5.03 4.23
  1. Root mean square deviation (RMSD) values were calculated between the docked ligand poses and the X-ray ligand based on heavy atoms. The entries in the table show the lowest RMSD values and associated AutoDock 4.0 scores for docked ligand poses of eight PDB complexes. Typically, the difference in RMSD between the all-atom and the polar-hydrogen model is very small; the average absolute difference is 0.20 Å. a AutoDock 4.0 Score