Immunogenicity B Cell Epiptope

Runs immunogenicity B-cell epitope evaluation on a batch of protein structures, predicting potential immunogenic regions using a sliding window approach.

Quick Start

1. Prepare your protein structure(s) in PDB format.
2. Set the desired window size for epitope prediction.
3. Run the node to obtain immunogenicity scores as a CSV table.

Setup Guide

1. Prepare Input Data

1. Ensure your protein structures are available in PDB format.
2. Load the PDB(s) using the appropriate node (e.g., Load PDB).

2. Configure Node Parameters

1. Specify the window size for the sliding window (default: 10).
2. (Optional) Adjust the mode for testing or mock runs if needed.

3. Run the Node

1. Connect the required inputs and execute the node.
2. Review the output CSV for immunogenicity scores.

Basic Usage

Predicting B-cell Epitope Immunogenicity

• Input one or more PDB structures.
• Set the window size to define the peptide length for prediction.
• Obtain a CSV table with immunogenicity scores for each input structure.

Configuration

Required Inputs

Field	Description	Type	Example
pdb	Structures to evaluate.	PDB	{"sample1": "...PDB content..."}
window_size	Sliding window size to construct peptides for prediction.	INT	10

Optional Inputs

None

Outputs

Field	Description	Example
score.csv	Immunogenicity scores of the proteins.	CSV file with scores

Best Practices

Input Preparation

• Ensure PDB files are properly formatted and contain valid protein structures.
• Use unique identifiers for each structure to avoid confusion in output tables.

Parameter Selection

• Choose a window size appropriate for the epitope length relevant to your study.
• For typical B-cell epitope prediction, a window size of 10 is standard, but adjust as needed.

Troubleshooting

Common Issues

• Empty or malformed PDB input: Ensure all input structures are valid and correctly formatted.
• No scores in output: Check that the window size is appropriate and input structures are not empty.

Need Help?

• Contact support for further assistance.