Q-Dock: low-resolution flexible ligand docking

Datasets:

• Training
• Benchmark

Generic protein-ligand interaction potential:

• Contact cutoffs
• Optimized parameters

Ligand docking against protein models:

• PDB-ID:
  PDB code and chain identifier of the target receptor protein.
• Threading templates:
  Weakly homologous structure templates identified by PROSPECTOR_3 used to generate theoretical receptor models by TASSER and to predict ligand binding sites by FINDSITE. Z-score and PDB-ID of the top-ranked template is given.
• Protein model:
  Theoretical model used as a target for ligand docking. RMSD from the crystal structure is calculated for CA atoms.
  *.all.pdb.gz - all-atom coordinates.
  *.cas.pdb.gz - coordinates for the simplified model (CA atoms and side chains centers of mass).
• FINDSITE pockets:
  The results of ligand binding site prediction for protein models using FINDSITE.
  *.findsite.dat - centers of predicted pockets. Top-ranked prediction was used by Q-Dock. [data format]
  *.potential.dat - pocket-specific protein-ligand interaction potential for top-ranked FINDSITE pocket derived from ligand-bound threading templates. [data format]
• Q-Dock (E_GEN):
  The results of flexible ligand docking by Q-Dock employing the generic force field (E_GEN). Final docked energy and simulation time (2.0GHz Opteron CPU) is given.
  *.Q-Dock_GEN.pdb - top-ranked low-resolution docking image generated by Q-Dock. [data format]
  *.rebuilt_GEN.pdb - all-atom model rebuilt from the low-resolution image.
• Q-Dock (E_TOT):
  The results of flexible ligand docking by Q-Dock employing the generic force field combined with the pocket-specific restraints (E_TOT). Final docked energy and simulation time (2.0GHz Opteron CPU) is given.
  *.Q-Dock_TOT.pdb - top-ranked low-resolution docking image generated by Q-Dock. [data format]
  *.rebuilt_TOT.pdb - all-atom model rebuilt from the low-resolution image.