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.

Ulpoad files one by one (up to 9 subunits):

  Number of subunits -the number of subunits in the complex to be modeled.
  For each subunit the user should provide the followings:

    Subunit id - a unique id for each subunit.

    PDB file - a file containing the structure of the subunit in PDB format.

    Transformations file - The transformations file contains the alternative positions for each subunit in space.
       The transformations file should have the following format:
       index    X-rotation    Y-rotation    Z-rotation    X-translation    Y-translation    Z-translation
       The rotation is around the X, Y and Z axes (in this order), and the angles are in radians.
       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.
       For example:

        1 2.11363 0.153389 2.82412 10.8802 -4.53751 -7.76723
        2 1.3353 -0.0999924 -2.60445 44.0002 4.52072 8.73591
        3 1.99255 0.159889 2.81949 12.0745 -2.47299 -9.35544
        4 1.3353 -0.0999924 -2.49973 43.5566 7.54644 8.73591
        5 1.32362 0.0314778 -2.64412 42.0512 3.61016 5.47968

Ulpoad zipped files:

    Pdbs zip - a zipped folder that contain a PDB file for each subunit.

    Transformations zip - a zipped folder that contain the transformations files for each subunit.

    index file - an index file indicating the name of the pdb file and transformations file for each subunit.
       The index file should have the following format:
       subunit_id    subunit_pdb_file_name   subunit_transforamtion_file_name
       For example:

        A 1WCM_A.pdb transA.txt
        B 1WCM_B.pdb transB.txt
        C 1WCM_C.pdb transC.txt
        E 1WCM_E.pdb transE.txt
        F 1WCM_F.pdb transF.txt

Number of output results - number of solutions to calculate.

Constraints file - constraints can be generated from the cross links data.
    The constrains file is not obligatory but if uploaded, it should have the following format:
    first_subunit_id    first_chain_id     first_residue_id     second_subunit_id     second_chain_id     second_residue_id     minimum_distance     maximum_distance
    For example:
    1 A 343 2 B 864 0.0 30.0
    1 A 343 2 B 886 0.0 30.0
    1 A 15 5 E 171 0.0 30.00
    2 B 191 3 C 149 0.0 30.0
    2 B 1057 3 C 199 0.0 30.0

Allow partial results - When this option is checked, the algorithm may return solutions that do not contain all the subunits. 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.

Generation of 3D transformations sets

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

Merge Solutions

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.

    index file - an index file indicating the name of the pdb file for each subunit.
       The index file should have the following format:
         subunit_id    subunit_pdb_file_name 
       For example:

        A 1WCM_A.pdb
        B 1WCM_B.pdb
        C 1WCM_C.pdb
        E 1WCM_E.pdb
        F 1WCM_F.pdb

    shared subunit - the subunit id of the common subunit.
The output is a zipped folder containing a transformations file for each subunit named trans_subunit_id.txt.