About DockingServer
DockingServer is an internet service that calculates the site, geometry and energy of small molecules interacting with proteins. You can dock your ligands to your proteins (see Flexible ligand docking) and analyze their interaction in 5 easy steps. The DockingServer is offered to everyone in the field of molecular modeling from beginners to professionals. DockingServer can be used for molecular docking and thorough analysis of single ligands or for high throughput docking of sdf files.

DockingServer is developed and maintained by Virtua Drug Ltd. Free access is provided for academic users without registration using a common workspace. Registration is required in order to get a private workspace. Data storage of the input and output files, high-priority jobs, e-mail and forum support are available upon payment (see pricing).

Molecular Docking
The task in molecular docking assignments is to find the best protein-ligand complex geometry. The problem is usually seen as an optimization task where the goal is to minimize the intermolecular interaction energy between the two molecules of interest. Since the possible number of protein-ligand complex geometry is usually very large, different algorithms are used in order to accurately explore the space of possible conformations while decreasing the computational power needed for the docking calculation at the same time. Thus, a molecular docking calculation consists of the following steps:
  • Optimization of the ligand geometry, calculation of pH-dependent partial charges, and identification of rotatable bonds
  • Calculation of electrostatic properties of the protein of interest and defining the ligand-binding region
  • The ligand-protein interaction is then calculated by a scoring function that includes terms and equations that describe the intermolecular energies. The result of a docking calculation is a ligand-protein complex geometry and the corresponding binding energy.
  • Therefore, for accurate interpretation of the results, a high-quality representation of the complex geometry is of great importance as well.
Features
Docking Server offers an easy way to compute ligand protein interactions or high-throughput virtual screening calculations in 5 easy steps
  • Step 1 - Ligand setup
  • Step 2 - Protein setup
  • Step 3 - Start of docking calculation
  • Step 4 - Evaluation of results
  • Step 5 - Preparation of Figures and Methods for your report
Docking Server offers an easy to use graphical interface for:
  • setting up and running molecular docking calculations,
  • advanced setting of the parameters used in docking calculations,
  • evaluating and presenting the results,
  • writing the method section for your reports,
  • organizing your docking data,
  • organizing your protein and ligand libraries,
  • searching within your ligand libraries according to chemical structure and physicalchemical properties
Softwares
  • DockingServer uses Autodock 4.0 for docking calculations (Autodock is a trademark of The Scripps Research Institute)
  • MOPAC 2007 is optionally used for calculating semiempirical charges and geometry optimization on the ligands
  • Marvin sketch, Marvin view and Chemaxon calculator plugins are used for drawing the ligand, and setting up for docking calculations
  • For representation of the resultant protein-ligand complexes, Jmol and VMD are integrated in Docking Server
Citing
In citing DockingServer, please refer to:
DockingServer
Bikadi, Z., Kovacs, S., Demko, L., Hazai, E.
www.dockingserver.com
Virtua Drug Ltd., Budapest, Hungary (2008)
AutoDock 4
Morris, G. M., Goodsell, D. S., Halliday, R.S., Huey, R., Hart, W. E., Belew, R. K. and Olson, A. J.
Automated Docking Using a Lamarckian Genetic Algorithm and and Empirical Binding Free Energy Function
J. Comput. Chem. 19, 1639-1662 (1998)
AutoDock 4 Scoring Function
Huey, R., Morris, G. M., Olson, A. J. and Goodsell, D. S.
A Semiempirical Free Energy Force Field with Charge-Based Desolvation
J. Comput. Chem. 28, 1145-1152 (2007)
MOPAC2007
Stewart, J. J. P.
OpenMOPAC.net
Stewart Computational Chemistry, Colorado Springs, CO, USA (2007)
Marvin
Marvin is used for drawing, displaying and characterizing chemical structures, substructures and reactions
www.chemaxon.com
Marvin 5.0, ChemAxon (2008)
Calculator Plugins
Calculator Plugins are used for structure property prediction and calculation
www.chemaxon.com
Marvin 5.0, ChemAxon (2008)
Jmol
Jmol: an open-source Java viewer for chemical structures in 3D
jmol.sourceforge.net
VMD
Humphrey, W., Dalke, A. and Schulten, K.
VMD - Visual Molecular Dynamics
J. Mol. Graph. 14, 33-38 (1996)
Liability Disclaimer
The result of any molecular modelling procedure is non-experimental and must be considered with care.