|Prediction of Complexes with Cn Symmetry by Geometry Based Docking
SymmDock Web Server
The web server runs SymmDock algorithm with default values.
- Unit Molecule: it is possible to
specify the PDB code of the unit 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.
- Symmetry Order: number of unit molecules in the multimer complex.
- 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.
Optional Input Fields:
- Binding Site: If you have
a credible data of potential contact residues between the monomers,
you may specify it as a list of residues in an uploaded file. The file has
to be in the following format: [residues index] [chain ID][newline]...
(if there is no chain ID then residue index is sufficient).
We suggest not to specify less than four residues. If you know only
one residue, insert its neighboring residues (surface residues) as well.
An example file site.txt:
- Distance constraints: The user can specify
distance constraints between pairs of atoms, one in one symmetric unit and
another in its copy. The distance constraints have to be given to the server in
the text file with the following format:
[atom_index1][atom_index2] [min_dist] [max_dist]
atom_index1 and atom_index2 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.
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 should
be within 5A from atom with index 377 and atom with
index 340 should be at the distance 5-10A from atom
with index 5603.
The ouput of SymmDock is a list of candidate complexes between user
specified receptor and ligand molecule. The list is presented to the
user in the format of a table, each table line represents one
- Solution No: Number of the solution
- Score: Geometric shape
complementarity score (see reference 1 for details). The solutions are
sorted according to this score.
- Area: Approximate interface area of
- ACE: Atomic contact energy
according to Zhang et al. (see reference 2).
- 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.
Download PDB files with complexes:
In addition, the server provides an option to download up to 100 top
ranking candidate complexes in the PDB format in one zipped file. The
user may specify the number of solutions and the server will prepare a
Zip file for download.
- Duhovny D, Nussinov R, Wolfson HJ.
Efficient Unbound Docking of Rigid Molecules.
In Gusfield et al., Ed. Proceedings of the 2'nd Workshop
on Algorithms in Bioinformatics(WABI) Rome, Italy,
Lecture Notes in Computer Science 2452, pp. 185-200, Springer Verlag, 2002
[ PDF file ]
- Zhang C, Vasmatzis G, Cornette JL, DeLisi C.
Determination of atomic desolvation energies from the structures of crystallized proteins.
J Mol Biol. 267(3):707-26, 1997
Beta 1.0 Version