Protein_charge_pI_calculator

This repository contains a Google Colab notebook for calculating the net charge and isoelectric point (pI) of proteins from user-provided PDB codes.

Protein Charge and Isoelectric Point Calculator

Author: Marilina Cathcarth

• Email: mcathcarth@gmail.com
• GitHub: mcathcarth

Version: 1.0

Date: Jun 10, 2024

Description: This script calculates the net charge and isoelectric point (pI) of proteins based on their sequences extracted from PDB files. The net charge of each protein is computed over a specified pH range, and the data is saved and visualized.

Citation

If you use this tool in your research, please cite this repository using the following DOI:

https://doi.org/10.5281/zenodo.11553881

For citation in various formats, please visit the DOI link.

Dependencies:

The script uses the following Python libraries:

• Biopython (Bio) - Licensed under the Biopython License Agreement (BPLA)
• NumPy - Licensed under the BSD License
• Matplotlib - Licensed under the BSD License
• requests - Licensed under the Apache License 2.0

Usage Instructions

1. Open the Colab Notebook: Click on the "Open In Colab" badge above to open the notebook directly in Google Colab.

2. Modify Input Parameters:

   • Update the pdb_codes list with the PDB codes of the proteins you want to analyze.

   • Optionally, provide user names (usr_names) and number of chains (usr_nc) if needed.

   • Set the parameters for pH_start, pH_end, pH_step, and target_pH as per your requirements.

3. Run Each Cell Sequentially: Ensure that you run each cell in order, as some cells depend on the outputs or definitions from previous cells.

4. View Results: After running the final cell, view the output which includes the isoelectric point (pI) and the net charge of each protein at the target pH. Additionally, a plot showing the net charge vs. pH will be generated and saved.

5. Save Your Work:

   • To save your changes, you can either:

     • Download the notebook to your local machine: File -> Download .ipynb

     • Save a copy to your Google Drive: File -> Save a copy in Drive

6. Note: Any changes you make in Google Colab will not affect the original notebook in this GitHub repository. Each user works on their own copy of the notebook.

Example Parameters

• pdb_codes: A list of PDB codes for the proteins to analyze (e.g., ["4F5S", "1CF3", "1OVA"]).

• usr_names: Optional list of user-provided names for the proteins.

• usr_nc: Optional list of the number of chains to consider for each protein.

• pH_start: Starting pH value for the range (e.g., 3.0).

• pH_end: Ending pH value for the range (e.g., 10.0).

• pH_step: Step size for the pH range (e.g., 0.1).

• target_pH: Specific pH value at which to calculate the net charge (e.g., 7.4).