Molecular docking
ChemSteck Gauss View 5 3D structure Ligand (*.stk) Avogadro or GAUSSIAN 09 Minimized 3D ligand (*.pdb) Openbabel Minimized 3D ligand (*.pdbqt) Protein Data Bank 3D structure protein (*.pdb) Quimera or Jmol or Protein or Preparation module in the Maestro program Free water, H-completed, minimized 3D protein (*.pdb) Openbabel Minimized 3D protein(*.pdbqt) Autodock Autodock Vina Autodock tools Glide Gold Molegro virtual docker Input data Output data
Affinity energies (*.txt) 3D protein-ligand (*.pdbqt) Openbabel 3D protein-ligand (*.pdb) Molegro Molecular Viewer APBS PyMol PDB2PQR server Electrostatic potential surfaces