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    Fast Interaction REfinement in molecular DOCKing

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Input Fields

There are two options for running the FireDock server:

  • Option 1 (use transformation file)
    • Receptor Molecule: PDB id and chain of the receptor (pdb:chain, e.g. 2kai:AB) or a file containing the structure of the receptor in PDB format.

    • Ligand Molecule: PDB id and chain of the ligand (pdb:chain, e.g. 2kai:I) or a file containing the structure of the ligand in PDB format.

    • Transformations File: (see example)
      A file containing the ligand's transformations in the following format:
      index X-rotation Y-rotation Z-rotation X-translation Y-translation Z-translation

      The rotation is around the X, Y and Z axes (in this order), and the angles are in radians.
      The translation parameters describe the movement of all the atoms of the ligand in the directions of the axes (X, Y and Z respectively) in Angstrom units.

      For example:
      1 2.11363 0.153389 2.82412 10.8802 -4.53751 -7.76723
      2 1.3353 -0.0999924 -2.60445 44.0002 4.52072 8.73591
      3 1.99255 0.159889 2.81949 12.0745 -2.47299 -9.35544
      4 1.3353 -0.0999924 -2.49973 43.5566 7.54644 8.73591
      5 1.32362 0.0314778 -2.64412 42.0512 3.61016 5.47968

  • Option 2 (use model file)
    • Models File: (see example)
      A file containing models of complexes for refinement in PDB format and the chains of the receptor and the ligand.
  • Number of output structures: The number of best solution structures (.pdb files) that will be generated.
    Please note that ALL the input comlexes are refined and their energies are shown in the output table. However, due to disk space considerations we can generate up to 100 refined PDB files.

  • e-mail address: An e-mail address for receiving the link to the results page. The results page will be available for at least a week.
IMPORTANT! please use standard PDB atom naming in the files you upload!

Advanced Input Fields

Setting this parameters is optional:
  • Complex Type: The type of the complex (Default, Antibody-Antigen or Enzyme-Inhibitor).
    This information is used for adjusting the scoring function.

  • Refinement Level: Restricted or Full.
    The restricted refinement mode allows only the clashing residues to be flexible. The full refinement mode allows all the interface residues to be flexible and uses an extended rotamer library. We recommend using the restricted mode at first, for coarse refinement, and on the final best candidates to use the full mode.

  • Number of RBO Cycles: The number of cycles for the rigid body optimization.

  • Atomic Radius Scale: Must be between 0 and 1. Affects the Van der Waals energy component in the scoring function. A low number allows a certain amount of clashes between the atoms. We recommend using 0.8 for coarse refinement and 0.85 for a final refinement of the best candidates.

  • Bound/Unbound: In a bound mode all the side-chains of the molecule are fixed

  • Fixed Residues Files: Files that specify fixed residues of the receptor and the ligand, in the following format:
    residue-index chain

    For example:
    88 A
    89 A
    90 A
    91 A

  • Flexible Residues Files: Files that specify flexible residues of the receptor and the ligand in the same format as the "Fixed Residues Files".
Output

see output example below:

The output is a table of all the input solutions, ranked by the global energy value. The refined complex structure is generated for up to 100 low-energy candidates. The user can view the complexes in the Jmol applet window and/or download the structures. The table can be sorted according to different properties:
  • Rank - according to the global energy.
  • Solution Number - according to the order of the transformations (option 1) or models (option 2)
  • Global Energy - The binding energy of the solution.
  • Attractive and Repulsive VdW - The contribution of the van der Waals forces to the global binding energy.
  • ACE - The contribution of the atomic contact energy (ACE) to the global binding energy.
  • HB - The contribution of the hydrogen bonds to the global binding energy.
The results page will be available for at least a week.
Receptor Ligand TransFile User e-mail
2kaiAB.pdb 2kaiI.pdb trans.txt duhovka@tau.ac.il
Rank Solution Number Global Energy
↓		 Attractive VdW Repulsive VdW ACE HB Structure show/hide
110 -87.13   -41.96     7.52      -14.04   -5.71  
29 -85.93   -41.29     6.12      -13.37   -4.85  
38 -27.50   -42.96     14.48      5.35   -3.68  
43 -26.41   -36.27     33.70      4.63   -9.06  
55 -18.66   -34.26     21.32      -1.57   -4.92  
61 -17.57   -42.02     35.06      4.83   -5.77  
77 -15.08   -27.43     17.51      2.12   -5.86  
86 -12.51   -28.48     15.19      7.33   -1.85  
92 -10.10   -41.38     46.78      -9.21   -3.71  
104 -6.47   -30.95     42.24      1.94   -2.82  
   
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