tomevault-io Version Compatibility
Reference examples tested with: MHCflurry 2.1+, numpy 1.26+, pandas 2.2+
Before using code patterns, verify installed versions match. If versions differ:
- Python:
pip show <package>thenhelp(module.function)to check signatures
If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.
Immunogenicity Scoring
"Rank my neoantigen candidates by immunogenicity" → Score and prioritize epitopes using multi-factor models combining MHC binding, proteasomal processing, expression level, and sequence foreignness for vaccine candidate selection.
- Python:
mhcflurryfor binding + processing predictions, custom scoring pipeline
Multi-Factor Scoring
Goal: Calculate a composite immunogenicity score from multiple weighted factors (binding, agretopicity, processing, expression, clonality, foreignness).
Approach: Score each factor on a 0-1 scale, then combine via weighted sum with domain-informed weights.
import pandas as pd
import numpy as np
def calculate_immunogenicity_score(peptide_data):
'''Calculate composite immunogenicity score
Factors considered:
1. MHC binding affinity (IC50)
2. Agretopicity (MT vs WT binding ratio)
3. Proteasomal processing
4. TAP transport
5. Expression level
6. Clonality (VAF for neoantigens)
7. Self-similarity (avoid tolerance)
Each factor scored 0-1, then weighted and combined.
'''
scores = {}
# 1. Binding affinity (lower IC50 = better)
# Transform to 0-1: 1 at 0nM, 0 at 5000nM
ic50 = peptide_data.get('ic50_nM', 500)
scores['binding'] = 1 - min(ic50 / 5000, 1)
# 2. Agretopicity (MT binds better than WT)
# Ratio of WT/MT IC50, capped at 10
agretopicity = peptide_data.get('agretopicity', 1.0)
scores['agretopicity'] = min(agretopicity / 10, 1)
# 3. Processing score (from MHCflurry)
processing = peptide_data.get('processing_score', 0.5)
scores['processing'] = processing
# 4. Expression (log scale, capped)
expression = peptide_data.get('expression_tpm', 10)
scores['expression'] = min(np.log10(expression + 1) / 3, 1)
# 5. Clonality (for neoantigens)
vaf = peptide_data.get('vaf', 0.5)
scores['clonality'] = vaf
# 6. Self-similarity (lower = better, less tolerance)
self_sim = peptide_data.get('self_similarity', 0.5)
scores['foreignness'] = 1 - self_sim
# Weighted combination
weights = {
'binding': 0.25,
'agretopicity': 0.20,
'processing': 0.10,
'expression': 0.15,
'clonality': 0.15,
'foreignness': 0.15
}
total = sum(scores[k] * weights[k] for k in weights)
return total, scores
Processing Prediction
Goal: Predict proteasomal cleavage and TAP transport probability for candidate peptides.
Approach: Use MHCflurry's Class1ProcessingPredictor to score peptide processing likelihood.
from mhcflurry import Class1ProcessingPredictor
def predict_processing_score(peptides):
'''Predict proteasomal cleavage and TAP transport
Processing score reflects probability that peptide will be:
1. Cleaved from protein by proteasome
2. Transported by TAP into ER
3. Loaded onto MHC
Higher processing score = more likely to be presented
'''
predictor = Class1ProcessingPredictor.load()
results = []
for peptide in peptides:
# Need surrounding sequence context for processing
# In practice, extract from protein context
pred = predictor.predict(peptides=[peptide])
results.append({
'peptide': peptide,
'processing_score': pred['processing_score'].values[0]
})
return pd.DataFrame(results)
Self-Similarity Assessment
Goal: Determine whether a candidate peptide resembles self-peptides, indicating potential T-cell tolerance.
Approach: Compute pairwise sequence identity against a proteome peptide set and flag high-similarity matches.
def calculate_self_similarity(peptide, proteome_peptides, threshold=0.8):
'''Check if peptide is similar to self-peptides
High similarity to self-peptides suggests:
- T-cells may be tolerized (deleted during development)
- Lower likelihood of immune response
Threshold 0.8 = 80% identity considered "self-like"
'''
def sequence_identity(seq1, seq2):
if len(seq1) != len(seq2):
return 0
matches = sum(1 for a, b in zip(seq1, seq2) if a == b)
return matches / len(seq1)
max_similarity = 0
most_similar = None
for self_peptide in proteome_peptides:
sim = sequence_identity(peptide, self_peptide)
if sim > max_similarity:
max_similarity = sim
most_similar = self_peptide
return {
'similarity': max_similarity,
'is_self_like': max_similarity >= threshold,
'closest_self': most_similar
}
Hydrophobicity at Position 2
Goal: Assess MHC anchor residue quality by checking hydrophobicity at key positions.
Approach: Check whether position 2 and C-terminal residues fall within the hydrophobic amino acid set preferred by HLA-A*02:01-like alleles.
def check_anchor_hydrophobicity(peptide):
'''Check hydrophobicity at MHC anchor positions
For HLA-A*02:01 and similar alleles:
- Position 2: Prefers hydrophobic (L, I, V, M)
- Position 9 (C-terminus): Prefers hydrophobic (L, V, I)
Strong anchors improve binding stability.
'''
hydrophobic = set('LIVMFYW')
pos2 = peptide[1] if len(peptide) > 1 else ''
pos_last = peptide[-1]
return {
'pos2_hydrophobic': pos2 in hydrophobic,
'pos_last_hydrophobic': pos_last in hydrophobic,
'anchor_score': (pos2 in hydrophobic) + (pos_last in hydrophobic)
}
Rank Epitopes
Goal: Rank epitopes by composite immunogenicity score and assign confidence tiers for prioritization.
Approach: Score all candidates, sort by immunogenicity, and assign high/medium/low tiers based on percentile ranking.
def rank_epitopes(epitope_df, top_n=20):
'''Rank epitopes by immunogenicity
Returns top candidates with scores and confidence tiers.
Confidence tiers:
- High: Top 5%, all factors favorable
- Medium: Top 20%, most factors favorable
- Low: Remaining, some factors favorable
'''
epitope_df = epitope_df.copy()
# Calculate scores
scores = []
factor_scores = []
for _, row in epitope_df.iterrows():
total, factors = calculate_immunogenicity_score(row.to_dict())
scores.append(total)
factor_scores.append(factors)
epitope_df['immunogenicity_score'] = scores
factor_df = pd.DataFrame(factor_scores)
# Combine
result = pd.concat([epitope_df, factor_df], axis=1)
# Rank
result = result.sort_values('immunogenicity_score', ascending=False)
# Assign tiers
n = len(result)
result['tier'] = 'low'
result.iloc[:int(n * 0.20), result.columns.get_loc('tier')] = 'medium'
result.iloc[:int(n * 0.05), result.columns.get_loc('tier')] = 'high'
return result.head(top_n)
Compare Candidates
Goal: Select a diverse set of vaccine candidates with broad HLA coverage and non-overlapping positions.
Approach: Iterate through ranked candidates, selecting those with non-overlapping genomic positions to maximize epitope diversity.
def compare_vaccine_candidates(candidates_df):
'''Compare and select vaccine candidates
Vaccine design typically selects:
- Multiple epitopes (5-20)
- Diverse HLA coverage
- High immunogenicity scores
- Non-overlapping sequences
'''
# Group by HLA coverage
hla_coverage = candidates_df.groupby('allele').size()
# Select diverse set
selected = []
used_positions = set()
for _, candidate in candidates_df.iterrows():
# Check for overlap with selected
pos = candidate.get('position', 0)
if not any(abs(pos - p) < 5 for p in used_positions):
selected.append(candidate)
used_positions.add(pos)
if len(selected) >= 20:
break
return pd.DataFrame(selected)
Related Skills
- immunoinformatics/mhc-binding-prediction - Binding affinity component
- immunoinformatics/neoantigen-prediction - Input candidates
- immunoinformatics/epitope-prediction - Epitope identification
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