Linker Conformation

Multi-frame trajectory or conformation playback for linker or complex structures. Load a preset or your own PDB IDs. To view a single ternary complex or component use the Ternary Complex Assembly or Component Alignment.

Start above: choose Preset and run, or enter your own PDB IDs / file URL / Morph pair; the viewer appears below after load.

Ternary Complex Assembly · Resources

Use your own PDB IDs or multi-MODEL file in the loader below, or see How to prepare your trajectory in the About section at the bottom.

Load a trajectory

Preset — built-in peptide–receptor demos. By PDB IDs / File URL — use your own binding pathway or multi-MODEL PDB (e.g. from MD). Morph — interpolate between two structures.

Peptide

Receptor

GLP-1 receptor

Auto-filled from selected peptide

Select a star product to view its binding trajectory. Data is pre-loaded for demonstration.

Press Enter in the dropdown to run. The lab viewer opens below.

Using your own data

By PDB IDs — One ID per frame, in order (e.g. binding pathway or key conformations). Loaded from RCSB.
By file URL — A single PDB with multiple MODEL … ENDMDL blocks (e.g. from MD or NMR). Use a path under public/ or a full URL.
Morph (A→B) — Interpolate between two structures (same atom count). Good for teaching or simple transitions.

Preset demos

Standalone examples (first is recommended for this site). Click Play in each card. For your own pathway or MD trajectory, use the loader above (By PDB IDs or By file URL).

Semaglutide & GLP-1 receptor

Key structures in GLP-1 signalling: peptide (PDB 6XBM) and GLP-1 receptor (PDB 7F9W). Conceptual two-frame view; replace with real binding trajectory for full reaction demonstration.

Frames: 6XBM → 7F9W (from RCSB PDB)

Small peptide structures

Two small peptide structures (2LL5, 1D4P) as a short trajectory. Illustrates multi-frame playback.

Frames: 2LL5 → 1D4P (from RCSB PDB)

B-DNA dodecamer

Classic B-form DNA (PDB 1BNA). Use for oligonucleotide and nucleic acid structure reference.

Frames: 1BNA (from RCSB PDB)

Ubiquitin

Small protein fold (PDB 1UBQ). Use for domain and secondary structure reference.

Frames: 1UBQ (from RCSB PDB)

Multi-MODEL PDB file (from public/)

Single file with multiple MODEL … ENDMDL blocks (e.g. from MD or NMR). To use your own: put the file in public/trajectories/ and use the loader above with By file URL.

File: /trajectories/demo.pdb (multi-MODEL PDB)

About this feature

Trajectories are pre-loaded or user-provided; no real-time simulation. Playback only.

How to prepare your own trajectory

PDB IDs: List structures in time or pathway order; each ID = one frame (from RCSB).
Multi-MODEL PDB: Export from MD/NMR software as one file with MODEL 1 … ENDMDL MODEL 2 …; put in public/trajectories/ or host elsewhere and use By file URL.

For single-structure viewing, see 3D Structure. Guide (reconstitution) · Peptide Library.