Docking
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
- Download the structure from PDB (here, 2BXA).
- Remove extra chains and hetatoms.
- 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
- 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. Bioinformatics, 32(20), 3142-3149.
Bioinformatics Programming
How to sort binding affinities based on a cutoff using vs_analysis.py script?

Previously, we have provided a Python script (vs_analysis.py) to analyze the virtual screening (VS) results of Autodock Vina. Now, we have updated this script to sort binding affinities based on user inputted cutoff value. (more…)
Docking
Virtual Screening using Autodock Vina: Frequently Asked Questions & Answers for Starters

Virtual Screening (VS) is one of the important techniques in bioinformatics. It can be easily performed using Autodock Vina. We have provided detailed articles on this topic. In this article, we are trying to answer some FAQs for beginners. (more…)
Docking
[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?
![[Tutorial] How to perform docking of zinc metalloproteins using Autodock Vina?](https://bioinformaticsreview.com/wp-content/uploads/2021/10/zn.jpg)
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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