Docking

In this module, users can prepare the structures of protein and ligands, and dock the ligands into the pocket of the receptor.

Structure preparation is achieved using AutoDockTools. Two docking programs (QuickVina and Smina) are provided for ligand docking. QuickVina is faster than Smina (about 2 fold) without compromising accuracy. Therefore, QuickVina is set as the default docking program and recommended when a great number of ligands are waiting to be docked.

To figure out where the biding site is, four methods are offered:

Reference ligand (default & recommended): upload a ligand whose coordinates is in the receptor pocket;
Pocket Residues: input the name and sequence number of the pocket residues to define the location of pocket (actually, inputting sequence number only is also enough for locating);
Coordinates (X, Y, Z): input the coordinates of the binding site's center;
None: input nothing and the server will take the last ligand in the uploaded ligand database as a reference ligand.

Docking Panel

Protein

.pdb

Ligand

.mol2

Binding Site (optional)

.mol2

Docking

Email (optional)

@

type	parameter	description
protein repair		repair protein structure [detail...]
bonds_hydrogens: build bonds and add hydrogens; bonds: build a single bond from each atom with no bonds to its closest neighbor; hydrogens: add hydrogens; checkhydrogens: add hydrogens only if there are none already; None: do not make any repairs;
del_nonstd_residue		delete every non-standard residue [detail...]
yes: delete any residue whose name is not in ['CYS', 'ILE', 'SER', 'VAL', 'GLN', 'LYS', 'ASN', 'PRO', 'THR', 'PHE', 'ALA', 'HIS', 'GLY', 'ASP', 'LEU', 'ARG', 'TRP', 'GLU', 'TYR','MET']; no: no deletion;
protein cleanup		remove necessary atoms [detail...]
non-polar hydrogens: merge charges and remove non-polar hydrogens; lone pairs: merge charges and remove lone pairs; water residues: remove water residues; chains: remove chains composed entirely of residues of types other than the standard 20 amino acids; standard: all the options mentioned above;
ligand repair		repair ligand structure [detail...]
bonds_hydrogens: adds hydrogens and builds bonds to any non-bonded atoms; bonds: build a single bond from each atom with no bonds to its closest neighbor; hydrogens: add hydrogens;(PyBabel is used for adding all hydrogens, not just polar-hydrogens;)
add_charge		add Gasteiger partial atomic charges [detail...]
yes: add Gasteiger partial atomic charges; no: If this option is used, the input ligand should already have partial atomic charges;
ligand cleanup		remove necessary atoms [detail...]
non-polar hydrogens: merges non-polar hydrogens by adding the charge of each non-polar hydrogen to the carbon to which it is bonded and then removes the non-polar hydrogen from the ligand molecule; lone pairs: merges lone-pairs by adding the charge of each lone pair to the atom to which it is 'bonded' and then removes the lone-pair; standard: all the options mentioned above;
search_space_size	Float	this value restricts where the movable atoms should lie
exhaustiveness	Integer	exhaustiveness of the global search (roughly proportional to time)
num_binding	Integer	maximum number of binding modes to generate

Example: Protein | Ligand | Reference Ligand | Result