Químio - Informática - Tutorial Docking II

Question 1

What is the difference between this tutorial (Docking II) and the last one (Docking I)?

Answer 1

In this tutorial you will repeat the experiment of the previous tutorial with a more recent (and more
automatic) version of Autodock: the Vina program. To run this program you need a) the .pdbqt files of
the ligand and the receptor you prepared in the previous tutorial and b) a conf.txt file with the
configuration of the docking experiment where you specify the center and size of the grid and the name
of the files. With Vina you don’t need to run the autogrid program: the maps with the interaction
energies of probe type atoms are automatically generated.

Question 2

The first step of the Docking II is the experimental setup. What is this for?

Answer 2

1. Organize Your Files:
   o You move the prepared ligand (ibp.pdbqt) and receptor (1EQG.pdbqt) into a clean working directory to keep everything organized for the Vina run.
2. Edit the Configuration File (conf.txt):
   o This file tells Vina how to perform the docking. You’re modifying it to:
    ✅ Specify the correct ligand and receptor filenames.
    ✅ Define the center of the search box — the area Vina will explore to place the ligand.
    ✅ Define the size of the search box — how big of an area around the center Vina will consider for docking.

Question 3

What is the difference between AutoDock Vina and AutoDock Tools?

Answer 3

Box size units: AutoDock4 uses grid points (0.375 Å per point); Vina uses Angstroms directly.

Setup files: AutoDock4 requires .gpf and .dpf files; Vina uses a single conf.txt.

Grid maps: AutoDock4 uses precomputed maps via AutoGrid; Vina calculates interactions internally.

Question 4

Now we are going to do docking of ligand IBP in the binding site. Tell me the steps for this

Answer 4

1. Open Command Terminal and Navigate to the Folder:
   o You’re moving to the working directory where your ligand, receptor, and conf.txt configuration file are stored. This is necessary to run Vina in the correct context.
2. Run the Docking Command:
   o The command runs AutoDock Vina using the instructions in conf.txt.
   o It outputs:
    ibp_out.pdbqt: contains the predicted ligand poses.
    log.txt: contains scores (estimated binding affinities) and pose rankings.
3. Analyze Results:
   o You open ibp_out.pdbqt in AutoDockTools or PyMOL to visualize the binding poses and compare them.
   o Use log.txt to assess:
    Binding energy estimates (lower = better).
    Pose similarity/differences, helping you identify the most likely binding conformation.
4. Compare with AutoDock4 Results:
   o This helps you evaluate whether the two tools agree on the binding mode and strength — useful for validation or decision-making.
5. Optional Help Command:
   o Use -help to see all command-line options Vina offers for advanced usage.