Practicum 3 - Protein-Ligand Docking

In this tutorial, you will be introduced to docking approaches by  undertaking on your own docking experiments on the androgen binding receptor seen in Practicum 1.  You will use Autodock vina, a flexible ligand-protein docking program which consists in an optimized version of the program Autodock. Some of the concepts detailed during the  theoretical courses are available in Autodock and the general procedure proceed in two steps: the calculation of the map of interactions of the binding site with some general atom types and the posing of the lligand respecting this map of interaction. We will set up the system and perform the calculation thanks to a novel interface available in UCSF Chimera. 

1. Ligand and Protein Set up

Autodock scoring function is applied using an adapted AMBER force field, the atoms of the protein and the ligand have to be set up in accordance with  this ff. You first have to generate the files you need for the docking: a receptor structure and a ligand structure. Open the 2ama structure in chimera. Then keep a mol2 file for the steroid on one side and the receptor on the other. Close the session. Open back the structures one by one. You can use the Dock Prep interface or use the Add the hydrogen to each structure (command line: addh).

3.Setting up the docking 
Go to the Tools-->Surface/Binding Analysis --> Autodock Vina

There you have to enter all the minimal information needed to proceed with the calculations:

- Output file: where the output will be located

- Receptor: select the receptor model you want for receptor

- Ligand: the same but for the ligand

This done, you need to define the location of the space for the prediction of the binding (binding site). To do so, check the resize search volume using (whatever the button is). Then play with the center button to generate the right size of the box.

Do not touch everything else and send the calculation.

4. Analysis
Once the calculation has finished we can analysis the conformations obtained and their energy.  The output will pop up. That's your turn to do the analysis and check to which point the prediction is adequate.


Part II

In the previous part of the tutorial, we focused on systems for which the crystal structure of the receptor is already well prepared for the docking of the ligand and provides with the best conditions for docking experiments:

1. we are dealing with holo form of the receptor

2. The cavity site is well defined and isolated from the solvent

3. There is no missing part of the receptor in the region of the binding site

4. The binding is mainly hydrophobic in nature


In this second part of the practicum, we will see how things are slightly less straigth forward when the complementarity between both partners is not that pre-established.


2. Cross docking

We will try to see to which level the structure of the receptor influences on the quality of the docking and how the complementarity protein-ligand is sensible.

2.1 repeat the docking experiment you previously carried out with the receptor with pdb code 2oz7

       Previous to docking observe the difference between 2oz7 and the conformations you worked on previously

       Analyse the results and compare with those of the last tutorial

2.2 Perform cross docking:

      dock the ligand of one of your initial systems (2amb, 2ama o 2am9) into 2oz7 and vice versa (you can spread other the classroom the different experiment to perform).

      Observe the variation in the results obtained when the structure of the ligand is not completely optimized to the structure of the receptor

3. relaxing the structure of the system. 

      one of the most complicated variables to deal with in docking are cycle optimization. Although many programs now incorporate optimization of rings, this is still a complex exercise. 

       take the structure of the steroid and apply a minimization of about 10000 step of steepest descent. Then dock back in the structure of the receptor. Any change?


Conclude on the overall process. 

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