Requirement of Input Docked Model File Format

Different docking softwares may have different output format of docked models. DockRank requires the following format of PDB files of Docked models.

  • The name of the files containing information on the complexes should not contain blank spaces.
  • We recomended to name files following the PDB standard (e.g. abcd.pdb).
  • The content on these files should have the same format used by ClusPro (as in the following example):

    •    1. In this format, ligand and receptors are enclosed by HEADER ... END labels

       2. The columns for the temperature factor (positions 61 - 66, see PDB specification) cannot be empty. Fake numbers such as 0.00 are accepted.

    An example docked model file generated by ClusPro : 
    HEADER receptor
ATOM      1  N   GLY A   2      25.503   1.260  58.635  1.00  0.00      RA0  N
ATOM      2  H   GLY A   2      24.880   0.503  58.449  0.00  0.00      RA0  H
....
ATOM   1214  N   LYS B   4      14.695   5.019 103.691  1.00  0.00      RB0  N
ATOM   1215  H   LYS B   4      13.879   4.438 103.673  0.00  0.00      RB0  H
...
END
HEADER ligand
ATOM      1  N   GLU A   6      37.988   9.067  91.869  1.00  0.00      LA0  N                          
ATOM      2  H   GLU A   6      37.189   9.618  91.627  0.00  0.00      LA0  H                          
...
END
    In this example, the receptor is composed by two chains (A and B), and the ligand is composed by one chain (A).

    For an example of docked models, please click here.