Modelling of multimolecular protein complexes. DockStar is an algorithm for modeling of multimolecular protein complexes. The input is the pdb files of the complex subunits, a set of alternative 3D transformations for each subunit and , if available, cross links constraints.
Input fields The server supports large number of subunits. The user can decide rather to upload the transformation and pdb files one by one or in a zipped file.
For each subunit the user should provide the followings: Subunit id - a unique id for each subunit. Transformations file - The transformations file contains the alternative positions for each subunit in space. The translation parameters describe the movement of all the atoms of the ligand in the directions of the axes X, Y and Z respectively in Angstrom units. Transformations zip - a zipped folder that contain the transformations files for each subunit. Constraints file - constraints can be generated from the cross links data.
This option should be checked if a transformations file does not contain at least one correct transformation. In this case it is preferred that this subunit will be missing from the output solution.
Job name - The name of this DockStar run. Email - An email address for receiving the link to the results page. The results page will be available for one month. For each subunit a set of alternative transformations is necessary. Each transformation represents an optional location of the subunit in the 3D space. These transformation sets can be generated by several methods, depending on the existing experimental data.
From a homolog protein complex - 3D alignement of a subunit in the complex to be modeled with a subunit in the homolog complex can retrieve a candidate location and hence, a candidate 3D transformation in the 3D space for this subunit. By docking - First, choose one subunit with the largest number of interacting neighbors to serve as an anchor subunit.
Then, dock all the anchor's neighboring subunits to the anchor, by PatchDock for example. In each docking run, set the anchor subunit as the receptor and the neighboring subunit as the ligand. The output transformations file of the docking method will serve as the input transformations file of the ligand subunit for DockStar. The anchor subunit transformations file should have only this line: 1 0 0 0 0 0 0. In some cases, the structural solution of a protein complex can be calculated iteratively.
First, the complex is divided to sub-complexes. Each is solved separately by DockStar. Top solutions of sub-complexes that share a common subunit can be merged and translated to new transformation sets. These transformation sets will serve as input for a new DockStar run that will generate structural solutions of the whole complex or of a bigger sub-complex.
The translation of top solutions of sub-complexes to transformation sets is supported under merge solutions. Input fields: Pdbs zip - a zipped folder that contain a PDB file for each subunit. Solutions zip - a zipped folder that contain the results tables to be merged and translated to transformations. Each results table can be downloaded from the DockStar output page.