ZDOCK PDB Marking and Output File







Docking sites



Here are the PDB columns marked by mark_sur.

  • 56-57: ACE type (ZDOCK 2.3) of 1-18, or IFACE type (ZDOCK 3.0) of 1-12 (according to parameters in uniCHARMM file). For blocked atoms, this value should be set to "19" after running mark_sur.
  • 63: Surface ("1") or non-surface ("0") atom (using 1 A^2 surface exposure cutoff).
  • 65-68: Atom radius.
  • 78-82: Atom charge.
Note: The message: "STOP INCREASE NCUBE" from mark_sur means that your protein is too large to be marked. It should be reduced in size if possible.

Here is an explanation of the fields in a ZDOCK output file.
Italics denote additions to the original ZDOCK file format, implemented in ZDOCK 3.0.2 and ZDOCK 2.3.2

  • Header lines: The first five lines (four lines for the original ZDOCK file format) provide the names of the input pdb files, as well as parameters for the initial positioning of the structures.
    • The first line is the size N of the NxNxN grid used in the docking, the spacing between grid cells (always 1.2 A), and whether the receptor or ligand was fixed during docking (0 = receptor, 1 = ligand).
    • The next line gives the initial rotation of the receptor in Euler angles.
    • The next line is the initial rotation of the ligand in Euler angles (this is non-zero if the seed is set using "-S seed" in the command line).
    • The next line is the receptor file, followed by its initial translation (x, y, z) to center.
    • The next line is the ligand file, followed by its initial translation (x, y, z) to center.
  • Rest of the file: After the header lines, each line describes a rotation and translation for the ligand with respect to its initial positioning.
    • The first three columns are the Euler angles (in radians) for rotating the ligand.
    • The next three columns are the grid positions describing the translation of the ligand with respect to its starting point.
    • The final column is the ZDOCK score (see the references for more on the ZDOCK scoring function).

    The predictions are sorted by ZDOCK score, with the predictions deemed better by ZDOCK found closer to the top of the file. The complexes generated by create.pl are numbered in this order as well (i.e. line number 6 provides complex.1, line number 7 provides complex.2, etc.).
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