Ring-Granular Model · Direct Kinematics

From DNA to 3D Protein
in Seconds

Upload a DNA sequence — get exact atomic 3D coordinates instantly. No folding simulation, no energy minimization. The ring-granular model computes each atom position directly from codons.

Try Free How it works
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64
Amino acid types
5
Helix types supported
PDB
Standard export format
Workflow

Three steps to your structure

No installation needed. Works entirely in the browser.

STEP 1

Upload EMBL file

Drag and drop your EMBL or GenBank DNA sequence file. Parsed securely — your data stays private.

STEP 2

Direct coordinate calculation

Each codon maps to a helix type and bond rotation angles. Direct kinematics gives exact atom coordinates instantly — no simulation, no energy minimization.

STEP 3

Visualize & export

Explore the structure interactively in cartoon, stick or sphere mode. Download the standard PDB file for further analysis.

Features

Everything you need

Interactive 3D viewer

Rotate, zoom and inspect your protein with 3Dmol.js — no plugins required.

Job history

All your predictions are saved. Revisit, re-download or compare results any time.

Secure & private

Files stored by UUID, JWT auth, bcrypt passwords. Your sequences never leave your account.

PDB export

Standard PDB format ready for PyMOL, UCSF Chimera, VMD and other molecular tools.

Cloud processing

Heavy computation runs server-side. Close the tab — your job keeps running.

Custom angles

Tune DNE rotation angles per-account for advanced structural calibration.

The science

Ring-granular model

The ring-granular model uses direct kinematics to determine protein structure from genetic code: each codon encodes a local helix type and bond rotation angles, from which every atom's 3D position is computed analytically — without any simulation.

The result is a complete set of atomic coordinates — backbone and side chains — ready in milliseconds per residue. Export as standard PDB and open in any molecular viewer immediately.

Codon → helix type + angles — deterministic lookup table
Direct kinematics — angles → exact XYZ, no energy minimization
Full atomic output — backbone + side chains as standard PDB
pipeline.py 
for i in range(0, len(dna), 3):
    b1, b2, b3 = dna[i:i+3]

    helix = DNE_GROUPS[b1][b2][b3]
    amino = DNE_AMI[b1][b2][b3]

    if amino == "TKD":  # stop codon
        break

    RotateAtoms(helix)
    AddAtoms(ATOMS_COMMON)
    AddAtoms(SIDE_CHAIN_MAP[b1*4+b2][b3])

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