Químio - Informática - Tutorial Docking I Flashcards
What softwares were needed for this tutorial?
AutoDock and Pymol
What were the required files?
Structure of protein (macromolecule, receptor): 1EQG.pdb
Structure of ligand (ibuprofeno): ibp.pdb
(to be copied to the same directory e.g. C:\ibp)
For the first step, we need to start AutoDocks. After this, we need to prepare our ligand. How so?
Menu “Ligand” → “Input” → “Open” . Choose files of type pdb and open the file ibp.pdb.
Click “OK”.
Menu “Ligand” → “Torsion Tree” → “Detect Root”.
To save the file, select “Ligand” → “Ouput” → and save as ibp.pdbqt (always save into the same
directory)
After we prepare our ligand we have to prepare our receptor. How so?
Select “Grid” → “Macromolecule” → “Open” . Choose files of type pdb and open the file 1EQG.pdb.
Click “OK” and save the file in the same directory of the previous files, as 1EQG.pdbqt.
Select “Grid” → “Set Map Types” → “Choose Ligand…” . Choose ‘ibp’.
How do we define the grid?
Select “Grid” → “Grid Box”. You may define the size of the grid with the first three wheels and the center of
the grid with the last three wheels. To center the grid on the ligand, use menu “Center” (of the small
window) and “Center on ligand”.
You may switch between show/hide the molecules with “Display” → “Show/Hide molecule…”.
To close the small window select its menu “File” → “Close saving current”.
Save a file with the grid specification: “Grid” → “Output” → “Save GPF” . Save the file in the same
directory of the previous files, as 1EQGibp.gpf
Purpose of the Grid:
Focus the docking search: Instead of scanning the entire protein surface, docking is restricted to the grid box area to reduce computational time and focus on the biologically relevant binding site.
Store precomputed interaction energies: The grid box contains precomputed energy values (electrostatics, van der Waals, etc.) for each point, making the docking process faster.
Guide the ligand placement: The ligand is moved and rotated within this box to find the best fit with the target.
Next we are going to pre-calculation the energy interactions with atom probes in the grid. What is AutoDocks doing during this?
AutoGrid computes energy grids for the docking process. These grids represent the interaction energy between each atom type of the ligand and the receptor at every point in the grid box you defined earlier in AutoDockTools.
Here’s a breakdown of what this step does:
1. Reads the grid parameter file (1EQGibp.gpf):
o Contains the size, center, and spacing of the grid box.
o Lists the atom types in the ligand.
o Specifies the receptor file to use for computing interaction energies.
2. Outputs a grid log file (1EQGibp.glg):
o Records details and diagnostics of the grid calculation.
o Useful for checking whether the grid setup completed successfully.
3. Generates multiple grid map files (e.g., .map, .d.map, etc.):
o Each map corresponds to a specific atom type in the ligand (e.g., carbon, oxygen, hydrogen).
o These maps store precomputed interaction energies used by AutoDock during ligand docking.
o This precomputation speeds up the actual docking run considerably.
After we run the experiment, we analyze the results. To save the best pose to later vizualize it on Pymol what do we do to get there?
- Load and Analyze Docking Results
* Open 1EQGibp.dlg: This is the docking log file generated by AutoDock after running the docking. It contains information about all the predicted ligand poses, their energies, and other metrics.
* Load Conformations: Brings all the docking results (poses) into the visualization environment in AutoDockTools.
* Play, ranked by energy: This animates through the different poses, from lowest energy (best binding) to higher energies. The lower the energy, the better the predicted binding. - Visual Aids and Pose Analysis
* Hide the macromolecule temporarily to better see the ligand docking.
* Choose and show macromolecule again to assess interactions.
* Show Info & Build H-bonds: Lets you explore docking pose details — hydrogen bonds, distances, residue interactions, etc. - Save the Best Pose
* Write Current: Saves the best pose (usually Pose 1, which has the lowest binding energy) as a .pdbqt file. This file represents the predicted bound conformation of ibuprofen.
After we analyze the results we vizualize the docking in Pymol. what is the purpose of this and how is it done?
- Open the following in PyMOL:
o The docked pose (.pdbqt)
o The original protein structure (1EQG.pdb)
o The starting ligand structure (ibp.pdb) - This allows you to:
o Compare the predicted binding pose with the experimental one.
o Visually examine which residues are interacting with the ligand. - Selecting → Residues mode lets you click on residues to identify them, helping you map the binding site and understand the key interactions (like hydrogen bonds or hydrophobic contacts).
