Peptide Designer

Build, visualize, and analyze amino acid sequences before sending them to quantum algorithms.

Overview

The Peptide Designer is BioQuantum's sequence construction workspace. It lets you build peptide sequences up to 100 residues using a visual drag-and-drop interface or direct sequence input, then inspect per-residue properties and 3D structure before dispatching to a quantum folding algorithm.

Amino Acid Palette

A grid of all 20 standard amino acids, color-coded by physicochemical property:

• Click any amino acid tile to add it to the Sequence Builder.
• Drag tiles directly into the sequence canvas.
• Hover a tile to see: full name, single-letter code, molecular weight, pKa (if charged).

Quick Input

For users who already have a sequence:

• Paste any valid FASTA or raw single-letter sequence (e.g., FVNQHLCGSHLVEALYLVCGERGFFYTPKA)
• Max 100 residues
• Press Ctrl+Enter or click "Load Sequence" to parse
• Click "Examples..." dropdown to auto-load pre-built sequences:
  • Insulin B-chain (30 residues)
  • GLP-1 peptide (26 residues)
  • Custom HP test sequences

Input rules:

• Only standard single-letter codes A–Y (20 amino acids) allowed.
• Spaces and line breaks are ignored automatically.
• Unknown characters are highlighted in red.

Sequence Builder

The drag-and-drop canvas shows your sequence as an ordered row of residue tiles.

• Reorder residues by dragging tiles left/right.
• Click a residue tile to select it → shows its properties in the right Properties Panel.
• Delete a residue: select it + press Backspace.
• Clear all: click the reset icon (top right of canvas).
• The sequence length counter (top right) updates live.

Properties Panel

When a residue is selected, the Properties Panel (top-right) shows:

The panel shows "Add residues to see properties" when no residue is selected.

Codon Optimization

Appears in the right panel after a sequence is loaded. Rewrites your peptide's implied codons to maximize expression in a target organism.

1. Load a sequence (Quick Input or Palette)
2. Click "Codon Optimization"
3. Select target organism: E. coli / Yeast / Human / CHO cells
4. Output: optimized DNA sequence (downloadable as .fasta)

Note: Codon optimization is independent of quantum folding — it operates on the DNA level, not structure.

3D Structure Viewer

Powered by NGL Viewer. Shows a real-time backbone model of the current sequence.

Secondary structure highlights:

• α-Helix → ribbon coil (blue by default)
• β-Sheet → flat arrow (yellow)
• Extended → straight strand

Controls:

• Rotate: left-click + drag
• Zoom: scroll wheel
• Pan: right-click + drag
• Reset view: circular arrow icon (top-right of viewer)
• Fullscreen: expand icon (top-right of viewer)

The viewer shows "Add amino acids to see structure" when the sequence is empty.

Sending to Quantum Fold

Once your sequence is built:

1. Click Send to Quantum Fold
2. The sequence is passed to the Quantum Models page
3. Choose your algorithm: VQE, QAOA, GroveFold, or Quantum Walks
4. The sequence is pre-filled — no need to re-enter