PatchDock and SymmDock: servers for rigid and symmetric docking

Abstract

Here, we describe two freely available web servers for molecular docking. The PatchDock method performs structure prediction of protein-protein and protein-small molecule complexes. The SymmDock method predicts the structure of a homomultimer with cyclic symmetry given the structure of the monomeric unit. The inputs to the servers are either protein PDB codes or uploaded protein structures. The services are available at http://bioinfo3d.cs.tau.ac.il. The methods behind the servers are very efficient, allowing large-scale docking experiments.

Figure 1

The PatchDock user interface. (A) The request form of PatchDock. The receptor molecule and the ligand molecule are given either by the PDB code of the molecule (chain IDs are optional) or by uploading a file in PDB format. (B) The solutions page presents the geometric score, interface area size and desolvation energy of the 20 top scoring solutions. The user can use the ‘show next 20’ button to view solutions of lower score. The user can download each solution by pressing the solution link in the rightmost column or download an archive file (ZIP format) of the best solutions using the action button at the bottom of the page.

Figure 2

The SymmDock request page and an example solution. (A) The request form of SymmDock. The asymmetric unit (the monomer) is given either by the PDB code of the molecule (chain IDs are optional) or by uploading a file in PDB format. The order of the symmetry must also be filled in. Once the request is submitted the prediction process begins. When it is completed, an email message with a link to a solutions page is sent to the user. The solutions page follows the same format as shown for PatchDock in Figure 1b. (B) A cartoon representation of a solution PDB file that was predicted and generated by SymmDock for a C₃ example.