Epitope Scout
Identify candidate surface epitopes for binder design. Upload a structure, select a chain, and get ranked patches scored by accessibility, hydrophobic exposure, rigidity, and hot-spot density.
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Structure file
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Parsing…
Target chain
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Predicted epitopes
| Rank | Score | SS | Res (RSA) | Residues | Flags |
|---|
Flag guide
Epitope score vs. design feasibility: Epitope score ranks binding potential based on surface chemistry, hot spots, and accessibility. Design feasibility assesses how difficult it will be to computationally design a binder, based on surface geometry, steric access, and glycan proximity. A high-scoring epitope can still be a challenging design target.
Known binders (PDB / SAbDab)
| PDB | Type | Organism | Resolution | Affinity | Contact residues | Epitope overlap |
|---|
How epitopes are scored
Each surface patch is ranked by a composite score (0–1) combining five structural determinants:
- 30% Hydrophobic exposure
- Hydrophobicity × mean RSA. Accessible hydrophobic surface drives desolvation ΔG. Chothia (1974); Vajda et al. (2018)
- 20% Structural order
- Independent secondary structure score. β-strands (1.0) and α-helices (0.8) are strongly preferred — they are rigid, geometrically regular, and dominate natural PPI interfaces. Loops score 0.2: flexible regions may rearrange in solution, causing binder design failure. Lo Conte et al. (1999); Fleishman et al. (2011)
- 20% Rigidity
- Inverted Z-scored backbone B-factor. Rigid, well-ordered epitopes incur lower entropic penalty upon binding. Carugo & Argos (1997)
- 15% Surface accessibility
- Inverted burial depth. Flat, moderately curved surfaces score high — the optimal topology for shape complementarity. Deep pockets and narrow crevices are penalized. Lo Conte et al. (1999); Lawrence & Colman (1993)
- 15% Hot spot density
- Fraction of Trp, Tyr, Arg, Phe, Lys, Asp, Glu. Core hot spots contribute >2 kcal/mol each; charged residues form salt bridges and H-bond networks. Bogan & Thorn (1998); Moreira et al. (2007)
Top 3 epitopes above quality threshold (score ≥ 0.40, ≥ 5 residues) are reported. Full data in CSV.