Calculating molecular surface...

Under the "Selected Binding Sites" there are shown predicted binding sites using ProBiS binding sites detection algorithm. These binding sites were predicted for the representative protein of the selected protein and mapped onto the selected protein. On default predicted binding sites are already selected for docking. Click "Remove" button if you want to change that.

You can add custom binding sites by selecting atoms and pressing Add binding site button. Small window will pop up in which you have to set radius of binding site. Depending on what atoms were selected their geometric center will be calculated. Binding site will include all atoms whose distance to geometric center is smaller than the chosen radius. Click Add Binding Site button to add selected binding site for docking. Click Cancel to cancel adding.

See user guide for more information.

Select Binding Sites

Select Parameters

Selected Binding Sites:

You can draw ligand structure with MarvinSketch application. To add ligand for docking click blue button with green plus icon in top toolbar. Ligands will be shown in in right side under "Ligands:". They can be removed with click on red x icon. When finished click on exit button.

If you are not familiar with MarvinSketch you can see user guide:
MarvinSketch User Guide

Draw Ligands

Ligands:

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Introduction

Candock is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.

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User's Guide

Related Citations

Predict the preferred orientation of ligands to a protein.

PDB ID: File: Chain ID(s):

Upload a PDB file Enter PDB ID

Ligands to Compare Against:

Upload a ligand database in file (mol2 or smi)

Choose ZINC database

Draw ligands structure

0 drawn ligands

Draw more ligands structure

Upload a ligand database in file (mol2 or smi) Choose ZINC database

Select Binding Site (mandatory)

0 selected binding sites

Advanced Parameters (optional) Advanced Parameters (optional)

Algorithm Parameters

Clus Rad:	Top Percent:
Interatomic	Excluded:
Grid:	Num Bsites:
Pos Tol:	Update Freq:
Max Iter Final:	Max Iter:
Mini Tol:	Fftype:
Max Num Possibles:	Iterative:
Max Allow Energy:	Docked Clus Rad:
Link Iter:	Max Possible Conf:
Tol Seed Dist:	Clash Coeff:
Spin:	Scale:
Step:	Cutoff:
Func:	Comp:
Ref:	Max Frag Radius:
Probis Min Z-Score:	Probis Min Pts:
Probis Clus Rad:	Neighb:
Max Num Ligands:	Tool Sed Distance:
Lower Tol Seed Distance:	Upper Tool Sed Distance:
Max Clique Size:	Num Univec:
Conf Spin:

Your e-mail address (optional):

A link to the results page will be sent to you by e-mail. Computation for a medium sized database will take a few hours.

Video Tutorial

Contact

Candock server was developed by Janez Konc, Tanja Stular and Gaurav Chopra as part of the CANDO project led by Ram Samudrala.