ParDOCK will predict the binding mode of the ligand conforming to the following format and other requirements:

  1. Upload hydrogen added Protein Reference Complex and Candidate Molecule in PDB format.
  2. Please make sure that Protein Reference Complex contains the Drug information to perform docking.
  3. Enter Formal Charge between +10 to -10. If no charge is entered, '0' will be assigned by default.
  4. Specify your email Id in text box. As the program might take 15-20 minutes to process the query, result will be e-mailed to you. If you don't specify any email id, result can be retrieved by Job ID which is provided at each submission. The job ID can also be used to check the current status of your job.
  5. Click Run to Submit the job. If other jobs are running on the server, your job will be put in queue and Job Status will be shown to you.

I. PDB FORMAT
 Some Useful Information about PDB: What is a PDB?

The term PDB stands for Protein Data Bank (http://www.rcsb.org/), the single worldwide repository for the processing and distribution of 3-D structure data for large molecules of proteins and nucleic acids. The PDB can refer to a data file provided here, or to any file following the PDB format. Files in the PDB include information such as the name of the compound, the species and tissue from which is was obtained, authorship, revision history, journal citation, references, amino acid sequence, stoichiometry, secondary structure locations, crystal lattice and symmetry group, and finally the ATOM and HETATM records containing the coordinates of the protein and any waters, ions, or other heterogeneous atoms in the crystal. Some PDB files include multiple sets of coordinates for some or all atoms. Due to the limits of x-ray crystallography and NMR structure analysis, the coordinates of hydrogen atoms are not included in the PDB.

Here are the ATOM records for the first two residues of ubiquitin from the 1UBQ entry in the PDB:

  A B C D E   F         G          H          I          J       K        L
ATOM 1 N MET 1 27.340   24.430   2.614   1.00    9.67   1UBQ   71
ATOM 2 CA  MET 1 26.266   25.413   2.842   1.00  10.38   1UBQ   72
ATOM 3 C MET 1 26.913   26.639   3.531   1.00    9.62   1UBQ   73
ATOM 4 O MET 1 27.886   26.463   4.263   1.00    9.62   1UBQ   74
ATOM 5 CB MET 1 25.112   24.880   3.649   1.00  13.77   1UBQ   75
ATOM 6 CG MET 1 25.353   24.860   5.134   1.00  16.29   1UBQ   76
ATOM 7 SD MET 1 23.930   23.959   5.904   1.00  17.17   1UBQ   77
ATOM 8 CE MET 1 24.447   23.984   7.620   1.00  16.11   1UBQ   78
ATOM 9 N GLN 2 26.335   27.770   3.258   1.00    9.27   1UBQ   79
ATOM 10 CA  GLN 2 26.850   29.021   3.898   1.00    9.07   1UBQ   80
ATOM 11 C GLN 2 26.100   29.253   5.202   1.00    8.72   1UBQ   81
ATOM 12 O GLN 2 24.865   29.024   5.330   1.00    8.22   1UBQ   82
ATOM 13 CB GLN 2 26.733   30.148   2.905   1.00  14.46   1UBQ   83
ATOM 14 CG GLN 2 26.882   31.546   3.409   1.00  17.01   1UBQ   84
ATOM 15 CD GLN 2 26.786   32.562   2.270   1.00  20.10   1UBQ   85
ATOM 16 COE1 GLN 2 27.783   33.160   1.870   1.00  21.89   1UBQ   86
ATOM 17 NE2 GLN 2 25.562   32.733   1.806   1.00  19.49   1UBQ   87

The fields seen here in order from left to right are the record type, atom ID, atom name, residue name, residue ID, x, y, and z coordinates, occupancy, temperature factor (called beta), segment name, and line number. Our drug design tool (i.e.; the tools available at SCFBio) requires only the information of ATOM and HETATM (i.e.; the coordinates of the ions) and fields starting from the record type to the x, y, and z coordinates. The user input for every tool is indicated thereof.

The general recognized format for our online tool can, thus, be outlined as:

12345678901234567890123456789012345678901234567890123
ATOM           1  N        MET           1            27.340     24.430     2.614
ATOM           2  CA      MET           1            26.266     25.413     2.842
ATOM           3  C        MET           1            26.913     26.639     3.531
ATOM           4  O        MET           1            27.886     26.463     4.263
ATOM           5  CB      MET           1            25.112     24.880     3.649
ATOM           6  CG      MET           1            25.353     24.860     5.134
ATOM           7  SD      MET           1            23.930     23.959     5.904
ATOM           8  CE      MET           1            24.447     23.984     7.620
ATOM           9  N        GLN           2            26.335     27.770     3.258
ATOM          10 CA      GLN           2            26.850     29.021     3.898
ATOM          11 C        GLN           2            26.100     29.253     5.202
ATOM          12 O        GLN           2            24.865     29.024     5.330
ATOM          13 CB      GLN           2            26.733     30.148     2.905
ATOM          14 CG      GLN           2            26.882     31.546     3.409
ATOM          15 CD      GLN           2            26.786     32.562     2.270
ATOM          16 OE1    GLN           2            27.783     33.160     1.870
ATOM          17 NE2    GLN           2            25.562     32.733     1.806

* Note: For every pdb entry, the spacing between each column should be exactly same as shown.

The pdb files can be graphically viewed by using certain softwares like Viewerlite, Mercury, Swissmol PDBviewer (spdv). To view the pdb files as shown above one need to open the pbd file using an editor (wordpad / notepad for windows or vi for linux based systems).

Thus, it can be summarized as:

The input file should be in the 'AMBER' PDB format i.e, as described here:

Note:

  1. There is a slight difference in the format for Protein Reference Complex and drug, as per PDB convention, this is shown below.
  2. The spacing between columns is not important but two columns should NOT merge at any place.

For Protein Reference Complex the format should be:

  A B C D E F     G                H               I             J
ATOM 1 N SER 1 42.653 -11.070     -13.991      1.00     0.00
ATOM 2 CA  SER 1 42.653 -11.070     -13.991      1.00     0.00
ATOM 3 2HB SER 1 42.653 -11.070     -13.991      1.00     0.00
ATOM 4 OG SER 1 42.653 -11.070     -13.991      1.00     0.00
ATOM 5 CA SER 1 42.653 -11.070     -13.991      1.00     0.00
ATOM 6 N SER 1 42.653 -11.070     -13.991      1.00     0.00
ATOM 7 CB SER 1 42.653 -11.070     -13.991      1.00     0.00
ATOM 8 2HD SER 1 42.653 -11.070     -13.991      1.00     0.00
TER
ATOM 8 C1 DRG 23 32.14 17.04    17.47      1.00     0.00
ATOM 8 H67 DRG 23 31.09 11.070    16.73      1.00     0.00

Where Column A represents the tag ‘ATOM’
Column B represents atom number
Column C represents atom name
Column D represents residue name
Column E represents residue number
Column F,G, H. represent the x, y, z coordinates respectively


 For Drug, the format should be:

A B C D E F G H I J
ATOM 1 C1 DRG 23 32.147 17.047 17.047 1.00    0.00
ATOM 2 H67 DRG 23 31.094 16.753 30.846 1.00    0.00
ATOM 3 H68 DRG 23 32.748 16.182 30.508 1.00    0.00
ATOM 4 H69 DRG 23 32.473 17.393 31.781 1.00    0.00
ATOM 5 N2 DRG 23 32.313 18.116 29.814 1.00    0.00
ATOM 6 C3 DRG 23 32.925 17.991 28.594 1.00    0.00

Where Column A represents the tag ‘ATOM’
Column B represents atom number
Column C represents atom name
Column D represents residue name
Column E represents residue number
Column F, G, H represent the x, y, z coordinates respectively

Please make sure that the drug file should not contain Sulphur(S) or Chlorine(Cl) atom as our program is not handling these atoms yet.

For any suggestion/comments/problem pl. contact scfbio@scfbio-iitd.res.in