There are two options for running the FireDock server:
- Option 1 (use transformation file)
- Receptor Molecule:
PDB id and chain/s of the receptor (pdb:chain, e.g. 1ukr:A) or
a file containing the structure of the receptor in PDB format.
Each residue of the receptor must have a unique number and chain.
The user can choose whether he wants to model backbone movements of the receptor or not
(model only side-chain refinement and minimization of the rigid body orientation).
- Ligand Molecule:
PDB id and chain/s of the ligand (pdb:chain, e.g. 1t6g:B) or
a file containing the structure of the ligand in PDB format. Each residue of the receptor must have a unique number and chain.
The user can choose whether he wants to model backbone movements of the ligand or not
(model only side-chain refinement and minimization of the rigid body orientation).
We recommend defining the smaller protein as the ligand, for better rigid-body minimization
IMPORTANT! please use standard PDB atom naming in the files you upload!
- Rigid Docking Solutions:
The server accepts two file formats of rigid docking solutions
* Users can use any other rigid-docking method and prepare a transformation file
according to the detailed PatchDock format.
* The server can process up to 100 transformations. Therefore, the output files
of PatchDock/ZDOCK must be trunked to contain only the first 1-100 best
solutions for further flexible refinement.
- Option 2 (use model file)
- 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.
Setting these parameters is optional:
- Perform SCO for:
Unchecking the boxes will keep side-chains of the molecule fixed
- SCO 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 normal modes: The maximal number of low frequency normal modes that the program will use in the refinement.
This parameter determined the amount of degrees of freedom of the backbone conformation, that the program will take into account during the refinement.
However, the lower this value is, the faster the program will run.
For example, if this parameter is set to 50, the program will refine the structure of the receptor by the most relevant normal modes among the 50 lowest frequency modes.
- Backbone flexibility level: This parameter determines the restriction of the backbone conformational change.
The lower it is, the more it prevents the backbone conformation to deform.
The flexibility level must be between 0 and 1.
- Number of MC Cycles:
The number of Monte-Carlo cycles for the rigid body optimization.
- Complex type: The type of the complex
(Default, Antibody-Antigen or Enzyme-Inhibitor).
This information is used for adjusting the scoring function.
- 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.
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