Last updated:  2013/11/24 (r216)
About Protein Docking Server
Protein Docking Server is an internet service that calculates the site, geometry and energy of proteins interacting with proteins. The Protein Docking Server is offered to everyone in the field of molecular modeling from beginners to professionals.

Protein Docking Server 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.

Molecular Docking
The task in molecular docking assignments is to find the best 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 complex geometries 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.
Protein Docking Server offers an easy way to compute protein-protein interactions in easy steps
  • Step 1 - Protein setup
  • Step 2 - Start of docking calculation
  • Step 3 - Evaluation of results
  • Step 4 - Preparation of Figures and Methods for your report
Protein 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 libraries
  • Protein Docking Server uses Autodock 4.0 for docking calculations (Autodock is a trademark of The Scripps Research Institute)
  • For representation of the resultant protein-protein complexes, Jmol and VMD are integrated in Protein Docking Server