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- 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.
- 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!
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".
- 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 file must not contain empty lines!!
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
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