Import molecules

After creating or opening project file, you will be allowed to import receptors and ligands. The Dockey supports various formats that can be read by OpenBabel.

Note

The Dockey will identify molecule file format through extension name. Please make sure that the molecule file extension is identical with its content.

Import Receptors

Import from local file

Go File menu -> Import Receptors to select receptor files and click Open to import into Dockey.

Import from PDB database

Go File menu -> Import Receptor from Database -> PDB to open a dialog:

pdb

Then input PDB IDs using comma to separate multiple ones and click OK button. The Dockey will automatically download the molecule from RCSB PDB database and import it.

Import Ligands

Import from local file

Go File menu -> Import Ligands to select ligand files and import to Dockey.

Import from SDF file

If you want to import all ligands from SDF file database. You can go to File menu -> Import Ligand from Database -> SDF to select the sdf file with multiple molecules to import.

Import from Zinc database

Go File menu -> Import Ligand from Database -> Zinc to open a dialog:

zinc

Then input Zinc IDs using comma to separate multiple ones and click OK button. The Dockey will automatically download the molecule from Zinc database and import it.

Import from PubChem database

Go File menu -> Import Ligand from Database -> PubChem to open a dialog:

pubchem

Then input PubChem IDs using comma to separate multiple ones and click OK button. The Dockey will automatically download the molecule from PubChem database and import it.

Import from ChEMBL database

Go File menu -> Import Ligand from Database -> ChEMBL to open a dialog:

chembl

Then input ChEMBL IDs using comma to separate multiple ones and click OK button. The Dockey will automatically download the molecule from ChEMBL database and import it.

Molecular List

The imported ligands and receptors will be separately displayed in molecular list.

mol

The molecular list has right-click menu.

molmenu

Delete molecules

You are allowed to use:

  1. Delete Current Molecule to remove current selected molecule.

  2. Delete All Receptors to remove all receptors from molecular list.

  3. Delete All Ligands to remove all ligands from molecular list.

  4. Delete All Molecules to remove all receptors and ligands from molecular list.

Filter and remove ligands

You are also allowed to use filter conditions to find molecules and remove them from molecular list.

ligfilter

You can use molecular weight, number of rotatable bonds and calculated logP to filter ligands. The ligands that math these filters will be removed from molecular list.

View molecule details

You can use View Molecule Details to obtain detailed information of molecule including number of atoms, bonds, heavy atoms, residues and rotors, formula, molecular weight as well as calculated logp.

molinfo

View molecule counts

You can use View Molecule Counts to view the number of receptors and ligands.

molnum