Prediction of Complexes with Cn Symmetry by Geometry Based Docking

SymmDock Web Server

The web server runs SymmDock algorithm with default values.

Input Fields:

• 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:
  88 L
  89 L
  90 L
  91 L
  92 L
  93 L
  95 H
  96 H
  101 H
  102 H
  

Output:

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 candidate complex.

Table Format:

• 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 the complex.
• 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.

References:

1. 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 ]
2. 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