pyDockSAXS Server

FAQ and Help


Tutorial

There is a pyDockSAXS server tutorial which you can follow here.

Moreover, a chapter with a complete description of the protocol has been published in Structural Bioinformatics.


Input data

pyDockSAXS uses three different files as input data:

  1. Receptor PBD structure. PDB files.
  2. Ligand PBD structure. PDB files.
  3. SAXS curve.

Email address

The email address is optional and only used to notify the user once the job has been finished.


Reference

To cite pyDockSAXS server, please reference “pyDockSAXS: protein-protein complex structure by SAXS and computational docking, B Jiménez-García, C Pons, DI. Svergun, P Bernadó and J Fernández-Recio. Nucleic Acids Research 2015; doi: 10.1093/nar/gkv368”


PDB structure files

We encourage to follow the PDB file format. Note that incomplete backbone or side-chain atoms may incur in inaccurate results and/or software failure.


SAXS data

Experimental SAXS input data is a file following this format:

  • First line is always ignored and treated as a title.
  • The following lines should contain three float values representing momentum transfer, non-zero intensity and standard deviation separated by blanks or commas. If standard deviations are not specified, they will be estimated automatically by CRYSOL (2% of the intensity values).
Example:

Title line
0.5000E-02   0.2064E+08   0.4227E+06
0.7500E-02   0.2053E+08   0.4200E+06
0.1000E-01   0.2115E+08   0.4161E+06
0.1250E-01   0.2090E+08   0.4112E+06
0.1500E-01   0.2077E+08   0.4054E+06
0.1750E-01   0.1971E+08   0.3986E+06
0.2000E-01   0.1945E+08   0.3909E+06
0.2250E-01   0.1898E+08   0.3823E+06
0.2500E-01   0.1832E+08   0.3730E+06
0.2750E-01   0.1897E+08   0.3631E+06
0.3000E-01   0.1737E+08   0.3525E+06
0.3250E-01   0.1676E+08   0.3414E+06
0.3500E-01   0.1632E+08   0.3298E+06
0.3750E-01   0.1629E+08   0.3179E+06
0.4000E-01   0.1497E+08   0.3058E+06
...

For more information, please see CRYSOL reference.


Previous docking results

pyDockSAXS server is able to reuse previous pyDockWEB server results via the rotation file. A rotation file describes how pyDock is able to translate and rotate a given ligand structure around a receptor structure. Each line of the rotation file is composed by:

  • Rotation matrix: the first nine terms describe the rotation matrix by row order (r11, r12, r13, r21, etc.).
  • Translation vector: the terms from ten to twelve indiciate the translation vector from the center of coordinates of the receptor structure.
  • Conformation: the last term identifies the number of receptor-ligand conformation.
pyDockWEB server provides a file with extension .rot for that purpose. Advanced users could filter those complex conformations by residue distance restraints or monomeric symmetry for example. 

  -0.956    0.004   -0.294   -0.277    0.325    0.905    0.099    0.946   -0.309   -2.306   -5.272   22.608      1
   0.223    0.712   -0.665   -0.063   -0.671   -0.739   -0.973    0.207   -0.105   -7.227   10.897   24.014      2
  -0.384    0.510   -0.769    0.791   -0.247   -0.559   -0.476   -0.824   -0.309    4.021   -8.084   28.232      3
   0.207   -0.743   -0.636   -0.230   -0.669    0.707   -0.951    0.000   -0.309   30.032   -1.054   34.559      4
  -0.780    0.504   -0.372   -0.175   -0.745   -0.644   -0.601   -0.437    0.669   18.081   -2.460  -10.433      5
  -1.000    0.000    0.000   -0.000   -1.000    0.000    0.000   -0.000    1.000    3.318    1.055   38.074      6
   0.420   -0.788   -0.450   -0.889   -0.258   -0.378    0.182    0.559   -0.809    8.239   -8.787   28.232      7
  -0.541    0.393   -0.743   -0.588   -0.809   -0.000   -0.601    0.437    0.669   26.517  -12.302    6.439      8
  -0.763    0.336    0.552   -0.513   -0.834   -0.201    0.393   -0.437    0.809   33.547   -7.381   16.281      9
  -0.856   -0.143   -0.497    0.507   -0.038   -0.861    0.104   -0.989    0.105    2.615   17.224    7.142     10

   ...

   0.105   -0.000    0.995    0.000    1.000    0.000   -0.995    0.000    0.105   41.983   14.412   -0.591    100

Result files

Once the computation has ended, the server prepares a gzip compressed tar archive containing several result files organized by folders as:

Note: "[xxx]" is a numeric identifier


input_data

This folder contains the original data provided by the user.


pydock

This folder contains the files generated by pyDock:

  • setup.log: a description of how pyDock reads and parses the original PDB structures provided by the user.
  • project_[xxx]_rec.pdb: receptor PDB structure parsed by pyDock.
  • project_[xxx]_rec.pdb.amber: AMBER force field values for atoms in receptor PDB structure used by pyDock.
  • project_[xxx]_rec.pdb.H: receptor PDB structure parsed by pyDock including hydrogens.
  • project_[xxx]_lig.pdb: ligand PDB structure parsed by pyDock.
  • project_[xxx]_lig.pdb.amber: same as receptor.
  • project_[xxx]_lig.pdb.H: same as receptor.
  • project_[xxx.rot: rotation angles for each of the poses generated by FTDock.
  • project_[xxx].ftdock: FTDock application output.
  • project_[xxx].ini: pyDock initialization file.
  • project_[xxx].ene: a table with a list of generated conformations scored and ranked by pyDock energy.
  • project_[xxx].saxs: a table with a list of Chi-square and the radius of gyration values for each generated conformation. When Chi-square is larger than 10, a 999.0 value is set in the file.
  • project_[xxx].ene.saxs: a table with a list of generated conformations scored and ranked by pyDockSAXS energy.

top100

This folder contains the top 100 structures scored by pyDockSAXS and their corresponding CRYSOL fit curve. File names follow the pattern "RankNumber_project_ProjectID_ConformationNumber.extension", where "RankNumber" corresponds to the "RANK" column and "ConformationNumber" to the "Conf" column in the results table.


fit_top10_SAXS

A folder containing the top 10 fit curves according to CRYSOL Chi-square value. The file name format follows the pattern "RankNumber_ConformationNumber.fit", where "RankNumber" corresponds to the "RANK" column and "ConformationNumber" to the "Conf" column in the results table.


Sample Data

You can download the sample data provided as example here: