The FireDock server addresses the refinement problem of protein-protein docking solutions. The method simultaneously targets the problem of flexibility and scoring of solutions produced by fast rigid-body docking algorithms. Given a set of up to 1000 potential docking candidates, FireDock refines and scores them according to an energy function, spending about 3.5 seconds per candidate solution.
The FireDock method includes three main steps:
- Side-chain optimization: The side-chain flexibility of the receptor and the ligand is modeled by a rotamer library. The optimal combination of rotamers for the interface residues is found by solving an integer LP problem. This LP minimizes a partial energy function consisting of repulsive van der Waals and rotamer probabilities terms.
- Rigid-body minimization: This minimization stage is performed by a MC technique that attempts to optimize an approximate binding energy by refining the orientation of the ligand structure. The binding energy consists of softened repulsive and attractive van der Waals terms. In each cycle of the MC method, a local minimization is performed by the quasi-Newton algorithm. By default, 50 MC cycles are performed.
- Scoring and ranking: This final ranking stage attempts to identify the near-native refined solutions. The ranking is performed according to a binding energy function that includes a variety of energy terms: desolvation energy (atomic contact energy, ACE), van der Waals interactions, partial electrostatics, hydrogen and disulfide bonds, π-stacking and aliphatic interactions, rotamer’s; probabilities and more.
There are two input options for the FireDock web server. In the first option, the user uploads or specifies codes of two Protein Data Bank (PDB) files (receptor and ligand) and provides a list of up to 1000 transformations (the required format is detailed in the Help page of the web server). Each transformation, when applied on the ligand, produces a candidate docking solution. In the second option, the user can upload an input PDB file, with each docking solution represented by a MODEL. The candidate solutions for FireDock can be generated by rigid-body docking methods, such as PatchDock, methods that use Fast Fourier Transform (FFT) such as ZDOCK, GRAMM-X, Hex etc.
In addition, the user may modify the ‘Number of output structures’ parameter. This parameter determines the number of best scoring candidates for which a PDB file with the refined structure will be generated. The server allows generating up to 100 PDB files. A link to the output web-page is sent to the email of the user as soon as the refinement process is finished.
The server includes optional advanced parameters for adjusting the refinement and scoring for a specific biological system. The user can specify the type of the complex (Default, Antibody–Antigen or Enzyme–Inhibitor), which is used for adjusting the weights of the scoring function. Furthermore, the user can specify if the proteins are in their bound or unbound conformation and if certain side-chains are known to be flexible or fixed.
Other advanced parameters determine the level of refinement. 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 to use the full mode on the final best candidates. The user can also set the number of rigid-body optimization cycles. This parameter influences the range of rigid-body movements around each original solution candidate. Finally, the user can scale the atomic radii used in energy calculations. This parameter influences the extent of acceptable steric clashes in the final refined solutions. We recommend using 0.8 for coarse refinement (‘Restricted’ mode) and 0.85 for a final refinement (‘Full’ mode) of the best candidates.
The output of the server is a table of all the input solutions, where each row corresponds to a single input complex. The table is sorted by global energy values. Refined complex structures are generated for up to 100 lowest energy candidates. The user can view the complexes in a Jmol applet window. Different complexes can be viewed simultaneously for comparison and the 3D structures can be downloaded as PDB files. The table can be sorted by different energy terms, such as the attractive and repulsive van der Waals forces, the ACE and the contribution of the hydrogen bonds (HB) to the global binding energy. An extended table with full specifications of the values of each energy term can be downloaded.