Protein of Interest

Protein of Interest (Target protein)

We talked about the protein selection in the previous tutorial. Kindly check out the previous tutorial here: Protein Target Selection

But we are going to talk about a particular protein here for molecular docking.

The protein of interest (target protein) is contingent upon the research question you aim to address. It is crucial to have a basic understanding of literature before choosing the protein of interest. Most of the time, target proteins in the three-dimensional structure are downloaded from the protein database "RCSB Protein Data Bank" at https://rcsb.org/.

For this tutorial, the three-dimensional (3D) crystallographic structure of Human SIRT6(PDB: 3K35) will be used; the structure will be retrieved from the protein data bank.

Access the Website

Go to www.rcsb.org

Search for 3K35 in the search bar (Figure 1).

Figure 1: Search for 3K35 on the Protein Data Bank

2. Click on Download (Figure 2)

Figure 2: Download of the protein structure

3. Download the PDB format (Figure 3).

Figure 2: Download of the PDB format.

After downloading the protein, the next thing is to clean the protein.

Protein Preparation

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