Molecular Mimicry & Cross-Reactive Autoimmunity

Molecular Mimicry

Antigen ↔ self-protein similarity 50%

How closely the pathogen's surface antigen resembles the body's own self-protein. Higher similarity means antibodies trained on the pathogen are more likely to also recognize — and attack — healthy self-tissue.

Simulation speed 1.0×

Readouts

Phase

Infection — clearing pathogen

Structural similarity

50%

Cross-reactive binding

–

Trained antibodies

0 / 12

Self-hits landed

Accumulated autoimmune tissue damage

How this mechanic works

Antibodies are trained against the pathogen's antigen shape (orange spikes, left). Once the pathogen is cleared, those same trained antibodies keep circulating and periodically test the self-protein markers on healthy tissue (cyan torus, right).

Binding is a shape match, not an identity check — so a self-protein that happens to look similar gets recognized too.
Both the chance a trained antibody binds self-tissue and the damage each hit causes scale with the similarity slider.
Tissue slowly repairs itself; damage only runs away when the cross-reactive attack rate outpaces that repair — which is exactly what high similarity does.

Pathogen

Self-tissue

Trained antibody Pathogen antigen Self-protein marker

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