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A fast practical - Small molecules.

Objectives of the practicum

  • Provide with the basic knowledge on the use of an advanced molecular visualizer
  • Provide with basics on practical skills of ligand based approaches and pharmacophore
  • Provide with basics on practical skills on protein-ligand dockings


This practicum will be performed using the program UCSF Chimera from the University of California San Francisco. Our practical will be performed on Linux and everything will be done using an updated version of UCSF Chimera. To do so, we need to install a series of add-ons on the last version of UCSF chimera in the user environment (not the pre-installed one).

Preliminary steps.

The UCSF Chimera version previously installed on the computers of the faculty of Sciences is not worthy for the use of this course. So, we need to install a new one.

To do so, first locate the UCSF Chimera homepage. Just google "UCSF Chimera" then go to the first link popping up and in the Downloads section. Then go to the Downloads section and download the binary (executable) file in 6 bits.

In a Linux terminal, define the correct environment for this new chimera installation:

export CHIMERADIR=/home/samba/homes/your-user/.local/UCSF-Chimera64-1.12

!!change your-user to the correct NIA.

The first thing you need to do is install a python environment optimized for the context of our practicum.

Follow the following steps:

Copy and paste the following line in a linux terminal

wget && bash Miniconda*.sh

When running this, follow the on-screen information and approve whatever you are asked.

Once all the installation has ended, run in the same terminal:
source $HOME/.bashrc

Then go to the webpage:

Download and uncompress the entire folder. Go to the green button “Clone or Download” and then download the zip file. Then go to the newly generated directory. Then in the terminal do: bash

You should be now able to run everything inside the chimera environment. Do not run the Chimera distro!

when working you need to be in a terminal window and do:

source activate insilichem (to activate the environment of the research group and in particular the updated version of UCSF Chimera)

pychimera --gui (to execute the new version of UCSF Chimera)

Once you have chimera running, activate the command line (Favorites --> Command line)

The system

The system we will work on is a family human hormone receptors. Students who have followed the Biosimulation class at the 4th year of the grade of chemistry of the UAB are used to it.  Have a bit of reading on the paper of the human androgen receptor binding protein;(HAR) (Pereira et al. or Cantin L. et al. or Askew E. et al.).


  1. Understanding HAR binding site.

    Look at the available structures of human androgen receptor binding protein at the Protein Data Bank (PDB - and download the structure of a HAR bound complexed with testosterone (2am9). Following the tutors’ comments, try to obtain a clear chemical map of the testosterone into the binding site of this receptor

     2. Ligand based analysis. Reaching a Pharmacophore

    The objective of this part of the work is to generate a pharmacophore for the ligands of HAR.

Once you have get used to with the initial structure, you have a better understanding of the main properties on recognition of the steroids with the receptor.

We will then generate a set of known molecules able to bind to the HAR. Using the PDB databank, the ligands have been extracted from the following structures: 2AMA, 2AMB, 1E3G, 2AX6, 2AX9, 3RLJ, 3RLL, 1E3K, 1XQ3, 4K7A, 2HVC

Download the molecules correctly prepared in the github depository


The first thing we will do is align the entire set of molecules. The alignment of molecules, especially when they have some kind of structural divergence, is a complex process on which computational scientists work with care.

The extension you have added to UCSF Chimera uses a library of programs dedicated to this problem. So, in the command line, write:

Command: open3align #0-12

This we align all the molecules. Mark down the Score that appears below the command line.

Discuss what you observe.

This alignment has been done purely on the structures extracted from the pdb. But one could expect on a ligand based problem that ligand with flexible groups could change their disposition. So, let’s do the same with the possible of the chemicals to rotate freely around their rotational bonds and explore ring conformers

Command: open3align #0-12 nConformers 10

Discuss what you observe both in term of the quality of the alignment AND the time of the execution.

To end with this part of the tutorial, we will now look at the generating different pharmacophores.

With the molecules aligned run the following command:

Command: p4 #0-12 mergeTol 1.5 minRepeats 3

P4 is the function to calculate the pharmacophore.

#0-12 the models (molecules) selected to have the calculation on.

mergeTol is the internal tolerance of the program to decide whether a given atom is should be considered in generating the pharmacophore.

minRepeats is the number of times that a feature should be kept.

Discuss the pharmacophore. Increase and decrease the magnitude of minRepeats. Explain in the classroom the origin of the difference observed.


As a final part of the exercise, we well now add the set with the Tamoxifen molecule, an antibreast cancer compounds. TO do so, we will go the pubchem database (google this).

There enter Tamoxifen for the search tool. Locate the PubChem CID index.

In UCSF Chimera go to Tools àBuild Structure. A new window opens. Select the PubChem CID and enter CID found in the PubChem database.

Once the tamoxifen loaded, eliminate all the hydrogens (del element.H) and realign the entire set.

Do you think tamoxifen owns the molecular features so to interact with HAR?


3. Protein-ligand dockings.

For this part of the practicum, what we aim at is perform the docking of tamoxifen to its receptor; the Estrogen receptor. Have a quick look at this receptor bound to estradiol (1qku). Then look at the same species bound to Tamoxifen (3ert).  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. 

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.

Preparing of the receptor structure.

To ease the process, follow the next steps:

remove all solvent and ligands: del ions

remove the ligands: del ligands

remove the solvent molecules: del water

remove the possible multimers: del @/altLoc=B

Go to Tools à Surface/Binding Analysis à Dock Prep

Once the windows pop, click yes and on the next window OK. This will add the hydrogens. On the next windows choose Gasteiger charges and OK.  This will add the charges.

On the final window give the name of the mol2 file you keep the structure in i.e. receptor_tamo

Preparation of the ligand.

Close all the models: close all

Open the pdb file 3ert: open 3ert

Keep only the ligand: sel ligand then del ~sel

Repeat the dock Prep procedure and save the ligand in a mol2 file i.e. ligand_tamo


Preparation and execution of the docking

Close the chimera session

Close all

Open the files

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).

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.


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.


Conclude on the overall process. 



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