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Code Description and Example Output

Brief Description

This code is a tool that researchers can use to understand the potential immune response caused by an antibody quickly. The user must have Python and the BioPython and Pandas library installed on their computer.

First, the user will download one of the two versions of the Python code to their computer. In version one (V1) of our code, the user will input a protein sequence (it does not have to be a full-length antibody) and in version two (V2), the user can input multiple protein sequences that are organized in a FASTA format. In V2, the user must input the protein sequences' file name and the output will be an excel file for each protein (details below).

Output

If the user is using V1, then they will be prompted to enter a protein sequence. They will enter the sequence and press enter to run the code (we used Jupyter notebook to run the file). The output will contain the antibody’s particular IgG subtype, the heavy chain constant region length followed by the heavy chain constant region sequence, and a table containing: affinity values (Kd) of each FcyR that it can bind to, the types of cells that express those particular FcyRs, and the effectors’ functions.

Examples : IgG1, IgG4, and small size antibodies

Alemtuzumab:

Dostarlimab:

Ofatumumab:

Using V2:

When the code is run, there will be an excel file created for each protein. The name of the excel file will match the header line of each protein in the fasta file.

In each excel file, there are two sheets named "data" and "info". The "info" sheet contains information regarding the IgG category, the heavy chain constant region length, and the heavy chain constant region sequence. The "data" sheet contains a list of multiple Fc receptors present in immune cells ("Name"), the binding affinity of the IgG antibody towards the receptor ("Affinity (1e6 M^-1)"), the immune cells that contain that receptor ("Cell Distribution"), and the effector function of those cells ("Effect").

Example: "FASTA_FDAantibody.txt"

Excel sheets generated:

Looking into "Trastuzumab heavy chain.xlsx " :

Sheet 1 (“info”)

Sheet 2 ("data")

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