Immunogenicity Class 1

Runs immunogenicity class 1 evaluation on the provided batch of proteins, predicting MHC class I binding and immunogenicity scores.

Quick Start

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

Setup Guide

1. Prepare Input Data

1. Generate or load protein structures in PDB format.
2. Ensure each structure has a unique identifier.

2. Configure Node Parameters

1. Set the c_allele to the desired MHC class I allele (e.g., HLA-A0101).
2. Adjust c_window_size for the sliding window (default: 9).

3. Run Evaluation

1. Connect the node in your workflow and execute to receive results.

Basic Usage

Immunogenicity Scoring

• Predicts immunogenicity for each input protein structure.
• Supports batch processing of multiple PDBs.
• Outputs a merged CSV table of scores.

Configuration

Required Inputs

Field	Description	Type	Example
pdb	Structures to evaluate.	PDB	See PDB doc
c_allele	MHC class I allele forming the pMHCI complex for prediction.	STRING	HLA-A0101
c_window_size	Sliding window size for peptide binding prediction.	INT	9

Optional Inputs

None

Outputs

Field	Description	Example
score.csv	Immunogenicity scores of proteins.	See CSV output

Best Practices

Input Preparation

• Use well-formed PDB files with unique IDs for each structure.
• Choose the appropriate MHC allele relevant to your study.

Parameter Selection

• Default window size (9) is suitable for most MHC class I predictions.
• Adjust window size only if you have specific requirements.

Troubleshooting

Common Issues

• Empty or invalid PDB input: Ensure all input structures are valid and uniquely identified.
• Incorrect allele format: Use standard allele names (e.g., HLA-A0101).

Need Help?

• Contact support for further assistance.