|Molecular Docking Algorithm
Based on Shape Complementarity Principles
PatchDock Web Server
The web server runs PatchDock algorithm with default values.
- Receptor Molecule: it is possible to
specify the PDB code of the receptor 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.
- Ligand Molecule: same as receptor 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 paramerters, 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 'receptor molecule'). In case of
protein-small ligand docking the algorithm uses parameter set
optimized for small size molecules.
The ouput of PatchDock 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
- Receptor Binding Site: If you have
a credible data of potential binding sites in the receptor, you may
specify it as a list of residues in an uploaded file. The file has
to be in the following format:
[residue 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:
- Ligand Binding Site: List the residues
of the ligand potential binding site. Look at the explanation of the Receptor Binding Site.
- Distance constraints: The user can
specify distance constraints between pairs of atoms, one in the
receptor ad one in the ligand. The distance constraints have to be
given to the server in the text file with the following format:
[receptor_atom_index] [ligand_atom_index] [min_dist] [max_dist]
receptor_atom_index and ligand_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.
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 (from receptor) should
be within 5A from atom with index 377 (from ligand) and atom with
index 340 (from receptor) should be at the distance 5-10A from atom
with index 5603 (from ligand).
- 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 1.3 Version