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Identifying binding sites in receptors using AutoSite tool

Tariq Abdullah

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Identifying binding sites in receptors using AutoSite tool

AutoSite is a computational method and tool that is used for the identification of binding sites of small molecules in target proteins [1]. It comes with the MGLTools2 package along with ADFR and AGFR. In this article, we will predict the binding sites in a receptor using the Autosite tool.

The potential binding sites in the receptor are computed and ranked as:

(No. of fill points X buriedness^2 )/(Radius of gyration)

We are using human serum albumin in this tutorial for binding site prediction.

Preparing receptor

  1. Download the structure from PDB (here, 2BXA).
  2. Remove extra chains and hetatoms.
  3. Prepare the PDBQT file of the receptor following the same procedure as used in the preparation of the receptor for docking. You can find a detailed procedure in this article. As you don’t need any grid file for this tutorial. Therefore, you can skip the grid box defining part for now.

Executing AutoSite

Open a terminal (Ctrl+Alt+T), change to the directory where you have saved your receptor PDBQT file, and type the following commands:

$ cd Downloads/

$ /home/user/Downloads/mgltools2_x86_64Linux2_1.0/bin/pythonsh /home/user/Downloads/mgltools2_x86_64Linux2_1.0/MGLToolsPckgs/AutoSite/bin/AS.py -r 2BXA.pdbqt

Don’t forget to replace the ‘user’ in the above command with your username.

As a result, it will output rank-based receptor files named as ‘_cl_<rank>.pdb‘ for the predicted pockets and ‘_fp_<rank>.pdb‘ for the predicted ligand.

References

  1. Ravindranath, P. A., & Sanner, M. F. (2016). AutoSite: an automated approach for pseudo-ligands prediction—from ligand-binding sites identification to predicting key ligand atoms. Bioinformatics32(20), 3142-3149.

 

Tariq is founder of Bioinformatics Review and CEO at IQL Technologies. His areas of expertise include algorithm design, phylogenetics, MicroArray, Plant Systematics, and genome data analysis. If you have questions, reach out to him via his homepage.

Docking

[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?

Dr. Muniba Faiza

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[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?

Proteins containing zinc atoms are docked in a different way than that of the normal simple proteins. Zinc atoms must be considered by a force field during the docking process. In this article, we are going to dock zinc metalloprotein with a ligand using Autodock Vina [1]. (more…)

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Docking

How to generate config file for docking using Autodock Tools?

Dr. Muniba Faiza

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How to generate config file for docking using Autodock Tools?

A configuration file is one of the required files for docking using Autodock Vina. In this article, we are going to generate a config file using Autodock Tools GUI [1]. (more…)

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Docking

How to install Autodock on Ubuntu (Linux) with CUDA GPU support?

Dr. Muniba Faiza

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How to install Autodock on Ubuntu (Linux) with CUDA GPU support?

Autodock [1] is most widely used for docking. To accelerate the docking process, especially, during virtual screening, Autodock-GPU [2] provides great help. In this article, we are going to install Autodock-GPU on Ubuntu. (more…)

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