UNICORNE Documentation

A guide to using the Unified Conformational Ensemble database for exploring multiconformational protein structures.

1. View Modes

UNICORNE offers two ways to browse protein structures:

UniProt View (default)

A flat list of all UniProt entries. Each entry contains the aligned monomeric and oligomeric structure ensembles that map to that UniProt ID. Best for exploring a specific protein.

Hierarchy View

Structures organized by fold and domain classifications. Navigate through Fold → Domain → UniProt → Structures. Best for exploring structural relationships across protein families.

Switch between views using the UniProt and Hierarchy buttons at the top of the sidebar.

2. Searching

Type in the search bar and press Enter to search. You can search by:

• UniProt ID — e.g., P00323
• Entry name — e.g., FLAV_NITV2
• Protein name — e.g., Flavodoxin
• Structure ID — e.g., 1AKQ

In hierarchy view, you can also search by fold name or domain name.

3. Filters

Click the filter icon button to open the filter panel. Filters differ between views. Set your desired range, then press Enter or search to apply.

UniProt View Filters

• Conformations — Number of available structure conformations
• Min-TM Score — The minimum pairwise TM-score among all aligned structures (0–1). Lower values indicate greater structural diversity.
• Protein Length — Number of amino acid residues
• Avg Coverage — Average fraction of the sequence covered by aligned structures (0–1)

Hierarchy View Filters

• Total Avg Angle — Average principal angle across all pairwise comparisons within the fold (degrees)
• Avg Seq Similarity — Average pairwise sequence identity among proteins in the fold (0–1)
• Direct UniProts — Number of UniProt entries directly assigned to the fold

All filters are double-sided range sliders. You can drag the endpoints or type exact values into the number fields.

4. UniProt Entries

Click on a UniProt entry to expand it. Inside each entry you will see:

• Entry Name and Protein Name — from the UniProt database
• Select All — Checks all structure checkboxes and starts the NMD animation in the normal mode viewer
• Clear — Unchecks all structures for this UniProt
• Share — Copies a direct URL to this UniProt entry to your clipboard
• Structure checkboxes — Check individual structures to load them. Clicking a checkbox loads the NMD animation for that UniProt in the normal mode viewer.

5. Normal Mode Viewer (Upper Panel)

Displays a single protein structure animated along its principal modes of conformational variation (PCA-based normal mode dynamics).

Animation Controls

Click the play icon (▶) to open the animation control panel:

• Play / Pause / Stop — Control animation playback
• Mode Selector — Choose which principal component mode to animate. Each mode shows its variance percentage (e.g., "Mode 1 (45.2%)")
• Frame Slider — Scrub through individual animation frames
• Speed — Adjust playback speed (1–100)
• Amplitude — Scale the magnitude of structural displacements (1–30)
• Loop — Toggle continuous loop on/off
• Show Vectors — Display displacement arrows showing the direction and magnitude of atom movement

Display Settings

Click the gear icon (⚙) to access:

• Color Scheme:
  • Displacement (default) — Colors by displacement magnitude. Red = minimal movement, blue = maximum movement. The legend shows values in angstroms (Å), scaled by the mode's eigenvalue.
  • Rainbow — Colors residues by sequence position (red at N-terminus → blue at C-terminus)
  • By Chain — Different color per chain
• Background — White, Black, Light Gray, or Dark Gray

Hover

Hover over any residue to see a green highlight on the Cα atom and an info bar showing Chain | Residue Name Residue Number.

6. Superposition Viewer (Lower Panel)

Overlays multiple selected structures for visual comparison. Click the Visualize button to load all checked structures.

Display Settings

Click the gear icon to access:

• Color:
  • By Structure (default) — Each structure gets a unique color
  • Rainbow — Residues colored by sequence position
  • Secondary Structure — Colored by helix / sheet / coil
  • By Chain — Different color per chain
• Style — Cartoon, Stick, Ball + Stick, Spacefill, or Trace
• Background — White, Black, Light Gray, or Dark Gray
• Show:
  • All structures — Shows all selected structures
  • 2 furthest (min TM) — Automatically loads only the two structures with the lowest pairwise TM-score (greatest structural difference)

Hover

Hover over any residue to see its info bar showing Structure ID | Chain | Residue Name Residue Number.

Fullscreen

Click the fullscreen button (⛶) in the top-right corner of either viewer to expand it.

7. Statistics Panels

Statistics appear in the right sidebar when you select a UniProt, fold, or domain. Click the ⓘ button next to any statistic for a detailed explanation.

UniProt Statistics (flat view)

• Length — Number of amino acid residues
• Avg Coverage — Average fraction of the sequence covered by aligned structures
• Max GLOCON Score — Highest principal angle, indicating maximum conformational diversity
• Max GLOCON IDs — The two structures with the maximum principal angle difference
• Min TM Score — Lowest pairwise TM-score (greatest structural divergence)
• Min TM IDs — The two structures with the minimum TM-score

Fold Statistics (hierarchy view)

• Total Average — Average principal angle across all pairwise comparisons
• Min Average — Most conformationally conserved UniProt
• Avg Min — Average of each UniProt's minimum principal angle
• Min Min — Lowest principal angle observed in the fold
• Avg Seq Similarity — Average pairwise sequence identity

Domain Statistics (hierarchy view)

• Total Average — Average principal angle within the domain group
• Min Average — Most conformationally conserved UniProt in the domain
• Avg Min — Average of each UniProt's minimum principal angle
• Min Min — Lowest principal angle in the domain

8. Global Controls

• Visualize — Loads all checked structures into the superposition viewer
• Download PDBs — Downloads all checked structures as individual PDB files
• Select All — Checks all visible structure checkboxes
• Clear All — Unchecks everything, stops animations, clears both viewers, and resets the Show dropdown
• Theme Toggle — Switch between dark mode (default) and light mode. Your preference is saved.

9. Icons & Indicators

• ★ Star — Appears next to UniProt entries that have normal mode animation data available. In hierarchy view, stars reflect availability for that specific fold context.
• Conformation count — Shown as (N confs) next to each UniProt, indicating the number of displayable structure conformations.
• Green dot — Status indicator at the bottom of the page showing the application is connected and data is loaded.

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UNICORNE — Center for AI in Protein Dynamics, Vanderbilt University