FoXSDock Help Page

Input Fields

• Receptor Molecule: it is possible to specify the PDB code of the receptor molecule or upload file in PDB format. Each code is a four character PDB ID, followed by a colon and a list of chain IDs, e.g. 2pka:AB. If no chain IDs are given, all the chains of the PDB file are used.
• Ligand Molecule: same as receptor molecule.

• SAXS profile: A file with experimental SAXS profile. The experimental file should have 3 columns: q, I(q) and error:

  #    q  intensity  error
  0.00000 3280247.73 1904.037
  0.00060 3280164.59 1417.031
  0.00120 3279915.19 1840.032
  0.00180 3279499.57 1566.084
  

  Header lines should be preceded by #.

  Please note that: q = (4π sin θ) / λ,
  where 2θ is the scattering angle and λ is the wavelength of the incident X-ray beam. If your experimental profile does not contain an error column, the server will add 5% error with Poisson distribution.
  Note, lines with zero intensities are skipped. If you profile contains negative intensity values, FoXS will read in the profile until it encounters the first negative intensity value.

• e-mail address: the link with the results of your request is sent to this address. Using this link you can view the docking results.
• Complex Type: PatchDock has different sets of parameters, optimized for different types of complexes. You can always use default complex type. In case of enzyme-inhibitor complex type, the algorithm restricts the search space to the cavities of the enzyme molecule. In case of antibody-antigen complex type, the algorithm automatically detects the CDRs of the antibody and restricts the search to these regions (note: the antibody should be specified as 'receptor molecule').
• Job name: if none is provided, the server generates a random name.
• Weighted SAXS score: if checked, the server will attempt to account for contributions from the receptor and ligand monomers in addition to the complex in the SAXS scoring. This option is useful for cases when the solution profile is a mixture of the two proteins and their complex.

• Distance constraints: The user can specify distance constraints between pairs of atoms, one in the receptor and one in the ligand. The distance constraints have to be given to the server in a text file with the following format:

  [receptor_atom_index] [ligand_atom_index] [min_dist] [max_dist]
  ...
  

  receptor_atom_index and ligand_atom_index are atom indices as specified in the PDB file (make sure there is only one atom with such index in your PDB). min_dist is the minimal distance allowed between the two atoms and max_dist is maximal.
  For example:

  25 377 0.0 5.0
  340 5603 5.0 10.0
  

  this file requires that two distance constraints will be satisfied in all the docking solutions: atom with index 25 (from receptor) should be within 5Å from atom with index 377 (from ligand) and atom with index 340 (from receptor) should be at the distance 5-10Å from atom with index 5603 (from ligand).

Sample Input

• Constructing a dimer of superoxide dismutase from the monomer (PDB 1hl5)
  Input monomer PDB - upload the same file as a receptor and as a ligand
  SAXS profile of the dimer - data from BIOISIS entry APSODP
  FoXSDock output - the dimer model that is close to native (Cα RMSD 1.75A) is ranked 4th.

Output Page

The output of FoXSDock is a list of complex models for user specified receptor and ligand molecule. The list is presented to the user in the format of a table; each table line represents one complex model. If you didn't receive any output models, this probably means that none of the docking-generated models fits the data well.

Table Format:

• Model No: Number of the model
• Z-Score: The z-score that combines interface energy and fit to the SAXS profile [1]. The models are sorted according to this score.
• SAXS χ score: χ score of the fit to SAXS profile for the model as calculated by FoXS [1-2].
• Energy score: Energy score as calculated by SOAP-PP statistical potential [3].
• Transformation: 3D transformation: 3 rotational angles and 3 translational parameters. The transformation should be applied on the ligand molecule.
• PDB file of the complex: The predicted complex structure in PDB format.

References

1. D. Schneidman-Duhovny, M. Hammel, and A. Sali.Macromolecular docking restrained by a small angle X-ray scattering profile. J Struct Biol. 2011. 173(3):461-71
2. D. Schneidman-Duhovny, M. Hammel, and A. Sali. FoXS: A Web server for Rapid Computation and Fitting of SAXS Profiles. NAR 2010.38 Suppl:W540-4.
3. G.Q. Dong, H. Fan, D. Schneidman-Duhovny, B. Webb, A. Sali. Optimized atomic statistical potentials: Assessment of protein interfaces and loops. Bioinformatics 29, 3158-3166, 2013.