💻PDB-CAT: A User-Friendly Tool to Classify and Analyze PDB Protein-Ligand Complexes
PDB-CAT is a program that classifies a group of protein-ligand structures into three categories: apo, covalent bonded, and non-covalent bonded. Besides the classification, the program can verify if there are any mutations in the protein sequence by comparing it to a FASTA sequence.
Open in Colab
STEP 0. Execute the Environment setup by JUST clicking on the ▶️ button.
It takes a few seconds

STEP 1. Import libraries by JUST clicking on the ▶️ button

STEP 2: Verify Required Folders
The script checks if the required directories exist. If they do not, it creates them automatically.
Here is where you should upload your cif files inside the cif-test folder!

Hover your mouse over the 'cif-test' folder and click the three-dot menu (or the options button) that appears next to it. From the dropdown menu, select the option to upload your files. Then, choose the files you want to upload from your computer and confirm the upload.
Step 3: Define Parameters
"""
=========
INITIAL INFORMATION. CHANGE THE CONTENT OF THESE VARIABLES IF NECESSARY
=========
"""
# Name of the folder with the cif files to process
folder_name = "cif-test"
# Chose a threshold for the number of amino acids, to discriminate between peptides and the subunits of the protein
res_threshold = 20
# Analyze mutations. True or False
mutation = False
# PDB code of the protein to analyze. If mutation is False, this variable is not used.
pdb = " "
```
Make sure all cells have been executed by playing the ▶️ button!
Download results in a zip
And that's it! If your computer downloads the zip file containing the results, the program has been correctly executed.
🚀 Learn how to use it with this example!
SARS-CoV-2 Main Protease

"""
=========
INITIAL INFORMATION. CHANGE THE CONTENT OF THESE VARIABLES IF NECESSARY
=========
"""
# Name of the folder with the cif files to process
folder_name = "Mpro"
# Chose a threshold for the number of amino acids, to discriminate between peptides and the subunits of the protein
res_threshold = 20
# Analyze mutations. True or False
mutation = True
# PDB code of the protein to analyze. If mutation is False, this variable is not used.
pdb = "SARS-CoV-2_FASTA"
🏁Output
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