Docking will be performed with three different programs:
Additional information about performing virtual screenings on Minerva
can be found
- Obtain/prepare a library of ligands to dock.
- One option to do so is the ZINC
website where you can ebter a ligand (either as a SMILES string or sketch it
and run a similarity serach to get a list of ligands that you can download
- ask for the ligands in .mol2 format.
- There are several libraries in the directory /sc/orga/projects/liglib.
A (somewhat outdated) desccripton of these directories is at the URL
the ligands have to be in mol2 format, and be placed in a separate directory,
one file per ligand. For Glide, the ligands have to be in a single file,
in SDF or .mae (Schordinger's Maestro) format.
The script set fullscreen has a program aggregate
that combines individual mol2 files into s single file
and program splitmol that
splits a single file into separate ligand files.
- Select a protein as a target, copy its PDB file in a new dirctory
where all dockings will be run
- Copy all files from ~mezeim01/fullscreen to the directory
where the PDB and PDBQT files are.
- Docking with Autodock-4 and Autodock-Vina:
- Prepare it for docking with Autodock-4 and Autodock-Vina using
for a tutorial on using ADT.
This preparation involves the following steps:
- Read in the protein
- Add hydrogens (polar only) or remove non-polar hydrogens (Edit menu)
- Assign Autodock4 types (Edit menu)
- Assign Gasteiger charges (Edit menu)
- Use the Grid menu to determine the size and position of the grid box.
This menu should put on the screen a box that you can manipulate
(translate or scale) with (virtual) dials.
Note the grid center and size; you will need it later (also for Glide!).
- Save the protein as a PDBQT file
(this format includes charges and the ATD4 types)
- If the total charge is not an integral number, use
to find the residues with non-integral charges.
If the deviations are a few hundredth then you can let Simulaid
fix it; otherwise fix them manually.
This latter may happpen when residues are incomplete
or atom names are not recognized or bonds are not considered by ADT.
- Execute the script
Select Autodock-4 - the script will later lets you run Autodock-Vina
Among others, it will prompt you for the target file name, the ligand file
directory and the information about the docking grid.
It will finish with submitting the jobs.
- Once the dockings finished, run the script getdir.csh
for all three programs - this should generate .dir files for each, containig
a list of docking result (log) files.
- Docking with Glide:
- Execute the script
- The file containing the ligands should be in .sdf format
(to be converted to .mae by the script).
- The grid center and size should be taken from the Autodock setup
- For each of the three programs, run
dockres - it will provide a lot
of information about the top-scoring ligands.
- Run the program
compligset to find out the concensus
- If you dock your ligands to two different proteins, compligset can find
ligands that are selectove to one or the other.