Immunogenicity MHC 2

Runs immunogenicity MHC class II evaluation on a batch of protein structures, predicting peptide binding and immunogenicity scores for specified MHC II alleles.

Quick Start

1. Connect a PDB batch to the node's input.
2. Specify the MHC class II allele and window size as needed.
3. Run the node to obtain immunogenicity scores as a CSV table.

Setup Guide

1. Prepare Input Data

1. Generate or load protein structures in PDB format.
2. Ensure all structures are properly formatted and batch IDs are unique.

2. Configure Node Parameters

1. Set the allele_name to the desired MHC II allele (e.g., DRB1*01:01).
2. Adjust window_size (default: 15) to control the sliding window for peptide prediction.

3. Run and Retrieve Results

1. Execute the node in your workflow.
2. Download or inspect the resulting immunogenicity scores CSV.

Basic Usage

Immunogenicity Scoring

• Predicts MHC II immunogenicity for each input protein structure.
• Supports batch processing of multiple PDBs.
• Outputs a merged CSV table with scores for all provided structures.

Configuration

Required Inputs

Field	Description	Type	Example
pdb	Structures to evaluate.	PDB	See PDB docs
allele_name	MHC class II allele for peptide binding prediction.	STRING	DRB1*01:01
window_size	Sliding window size for peptide prediction (11–30, default: 15).	INT	15

Optional Inputs

None

Outputs

Field	Description	Example
score.csv	Immunogenicity scores of the proteins.	See below

Best Practices

Input Preparation

• Use unique IDs for each PDB in a batch to avoid result merging issues.
• Validate PDB formatting before running the node.

Parameter Selection

• Choose allele_name relevant to your biological context.
• Adjust window_size based on peptide length of interest (typically 15 for MHC II).

Troubleshooting

Common Issues

• Empty or malformed PDB input: Ensure all input structures are valid and non-empty.
• Incorrect allele name: Use standard allele nomenclature (e.g., DRB1*01:01).
• Window size out of range: Set window_size between 11 and 30.

Need Help?

• Contact support for further assistance.