PatchDock

Antigen Molecule

It is possible to specify the PDB code of the antigen 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.

Antibody Molecule

Same as antigen molecule.

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.

Clustering RMSD

The value of the RMSD used for final clustering. The higher the value, the smaller the number of the results you get. The recommended values are 4A for protein-protein docking and 1.5A for protein-small molecule docking.

Complex Type

PatchDock has different sets of parameters, optimized for different types of complexes. You can always use default complex type. In case of enzyme-inhibitor complex type, the algorithm restricts the search space to the cavities of the enzyme molecule. In case of antibody-antigen complex type, the algorithm automatically detects the CDRs of the antibody and restricts the search to these regions (note: the antibody should be specified as 'antigen molecule'). In case of protein-small antibody docking the algorithm uses parameter set optimized for small size molecules.

Antigen Binding Site

If you have a credible data of potential binding sites in the antigen, you may specify it as a list of residues in an uploaded file. The file has to be in the following format: [antigen_atom_index] [antibody_atom_index] [min_dist] [max_dist] .... (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:

Antibody Binding Site

List the residues of the antibody potential binding site. Look at the explanation of the Antigen Binding Site.

Distance Constraints

The user can specify distance constraints between pairs of atoms, one in the antigen and one in the antibody. The distance constraints have to be given to the server in the text file with the following format: [antigen_atom_index] [antibody_atom_index] [min_dist] [max_dist] ...

antigen_atom_index and antibody_atom_index 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.

For example:

This file requires that two distance constraints will be satisfied in all the docking solutions: atom with index 25 (from antigen) should be within 5A from atom with index 377 (from antibody) and atom with index 340 (from antigen) should be at the distance 5-10A from atom with index 5603 (from antibody).

The output of PatchDock is a list of candidate complexes between the user-specified antigen and antibody molecule. The list is presented to the user in the format of a table, where each row represents one candidate complex. The format of the table is as listed below.

1. 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
2. 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