Predict chicken MHC Class I & Class II peptide binding
Upload a protein sequence or FASTA file and rank candidate peptides by predicted binding probability — built for vaccine developers, immunologists, and computational biology labs.
Choose a Module
Three independent prediction modules, one platform.
BioAnchorFormer
Trained CNN + Transformer model. Rank candidate 8–11-mer peptides by predicted MHC Class I binding probability.
MHC-II Predictor
Trained BiLSTM model. Independently scores BLB1 and BLB2 binding, displayed as BLB1, BLB2, Shared, or Negative.
Proteome Scan
Upload a multi-protein FASTA (e.g. a whole bacterial proteome). Get the best individual peptides overall, and which proteins are richest in epitopes.
About the Platform
This platform hosts three independent prediction modules for chicken MHC peptide binding. BioAnchorFormer is a transformer-based deep learning model purpose-built for MHC Class I peptide binding prediction, combining sequence-level representation learning with an anchor-aware attention mechanism that emphasizes the residue positions known to dominate peptide–MHC binding affinity (typically P2 and the C-terminal anchor).
The MHC-II Predictor classifies candidate peptides into four classes — BLB1, BLB2, Shared, or Negative. Given any protein sequence, each single-protein module generates overlapping peptide windows, scores every candidate, and returns ranked results. Proteome Scan runs the same models across every protein in a multi-FASTA file at once, surfacing both the best individual peptides and the richest proteins — helping researchers prioritize epitopes for downstream validation in vaccine design and immunotherapy pipelines.
Features
Everything a research lab needs to go from sequence to ranked binding predictions.
Flexible Input
Paste a raw protein sequence or upload a .fasta / .fa file directly.
Configurable Peptide Lengths
Choose from the peptide window sizes supported by each module.
Live Progress Tracking
Watch prediction progress, status, and estimated time remaining in real time.
Searchable Results
Instantly search, sort, and paginate through ranked peptide predictions.
One-Click Copy
Copy any peptide sequence to your clipboard for downstream tools.
CSV & Excel Export
Download full ranked results as CSV or Excel for offline analysis.
Dark & Light Mode
A clean, responsive interface that adapts to your working environment.
Validated & Secure
Strict input validation, file checks, and rate limiting protect every run.
How It Works
From raw sequence to ranked binding predictions in five simple steps.
Choose a Module
Pick MHC-I (BioAnchorFormer) or MHC-II prediction.
Provide a Sequence
Paste a protein sequence, upload a FASTA file, or paste a peptide list.
Choose Peptide Lengths
Select which peptide window sizes to generate and score.
The Model Scores Peptides
The module encodes each candidate peptide and predicts binding.
Review Ranked Results
Explore, search, visualize, and export high-confidence binding peptides.
Team
The BioAnchorFormer project is developed by a cross-disciplinary team spanning immunology, machine learning, and software engineering.
Sarathkumar Devaraj
Researcher Student • UTA IMSE PhD Student
Dr. Shouyi Wang
Supervisor • UTA IMSE Faculty
Dr. Stephen N. White
Collaborating Scientist • USDA
Contact
Questions about collaboration, model access, or the underlying research? Reach out.