ParDOCK will predict the binding mode of the ligand conforming to the following format and other requirements:
- Upload hydrogen added Protein Reference Complex and Candidate Molecule in PDB format.
- Please make sure that Protein Reference Complex contains the Drug information to perform docking.
- Enter Formal Charge between +10 to -10. If no charge is entered, '0' will be assigned by default.
- 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.
- 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:
- There is a slight difference in the format for Protein Reference Complex and drug, as per PDB convention, this is shown below.
- 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 |
32.140
| 17.040 17.470 1.00 0.00 |
| ATOM
| 8 |
H67 |
DRG |
23 |
31.090
| 11.070 16.730 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
