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Protein Core-Packing Designer

Simulated annealing designs an amino-acid sequence on a fixed four-helix-bundle backbone, packing hydrophobic residues into the buried core and polar/charged residues onto the solvent-exposed surface -- the knobs-into-holes principle behind real de novo protein design.

Molecular Biology3DAdvanced60 FPS📱 Mobile-adapted

De novo protein design starts from a target backbone shape and asks: which amino acid belongs at each position? This simulator fixes a four-helix-bundle backbone and uses Metropolis Monte Carlo simulated annealing to search amino-acid identity space, minimizing an energy function built from two real design principles: hydrophobic residues are rewarded for burying themselves in the bundle's core (knobs-into-holes packing against the other helices) while polar and charged residues are rewarded for sitting on the solvent-exposed surface, and same-charge residues are penalized for ending up close together at helix-helix interfaces. Watch a random starting sequence anneal into an organized hydrophobic core with a polar, charge-balanced shell — the same objective that guided the first computationally designed stable proteins.

⚙ Under the hood

Simulated annealing designs an amino-acid sequence on a fixed four-helix-bundle backbone, packing hydrophobic residues into the buried core and polar or charged residues onto the solvent-exposed surface -- the knobs-into-holes principle behind real de novo protein design.

protein designsimulated annealinghydrophobic coremolecular biologybiochemistrycomputational biology

3D · Three.js / WebGL renderer · 60 FPS target · runs fully client-side, no install