Catalytic Motif Scaffolding: Diffusion-Designed Enzyme Backbones

Catalytic Motif

Active-site preset

Scaffold length 70 res

Guidance strength 70%

Generation speed 1.0×

Denoising: 0%t = 1.00

Live Readouts

Catalytic geometry RMSD

— Å

Backbone clashes

—

Noise level σ(t)

— Å

How it works

This mirrors the core idea behind AI enzyme-design tools such as RFdiffusion "motif scaffolding": a diffusion model is trained to denoise random 3D coordinates back into a plausible protein backbone, and at generation time it is conditioned on a small set of fixed catalytic residues whose relative 3D geometry — not their position in the sequence — defines the active site.

x_t = x_0 + n_i · σ(t),   σ(t) = σ_0 · sin(t·π/2)
motif residues:  σ_motif(t) = σ(t) · (1 − g·0.85)
geometry error:  RMSD = sqrt( mean_ij (d_ij(t) − d_ij*)² )

Here t runs from 1 (pure noise) to 0 (fully denoised), x_0 is the sampled target structure, and d_ij* are the ideal pairwise distances between catalytic residues (e.g. the ~5-7 Å triangle of a Ser-His-Asp triad). The guidance strength g controls how tightly the sampler pins those residues to the ideal geometry — at g = 100% the final catalytic RMSD is near zero; at g = 0% the motif denoises with the same freedom as the rest of the chain and the active-site geometry drifts, producing a scaffold that folds correctly but can no longer catalyze anything.

Preset — swaps the target catalytic geometry: a 3-residue triad, a 3-ligand metal-coordination site, or a 2-residue dyad.
Scaffold length — how many residues fold around the fixed motif; longer chains need more loop/helix connective material.
Guidance strength — the classifier-guidance-style conditioning weight; watch the catalytic-RMSD readout diverge as it drops.
Backbone clashes — non-adjacent residue pairs (|i−j| ≥ 3) closer than 4.0 Å, a simplified steric-clash score used to flag physically implausible folds mid-denoising.
Generate new sample — redraws the stochastic backbone and residual motif offset, exactly like re-running a generative sampler for a fresh design candidate.

Catalytic motif residues Scaffold backbone Ideal motif geometry (dashed)

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