Visual SmallMolConformer Preview
Multi-frame 3D demos: load a preset or your own PDB IDs to see trajectory playback. Use Play/Pause and frame controls. To view and export 3D for your own SMILES, use SMILES to 3D.
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.
Auto-filled from selected peptide
Select a star product to view its binding trajectory. Data is pre-loaded for demonstration.
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 … ENDMDLblocks (e.g. from MD or NMR). Use a path underpublic/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).
Small peptide structures
Two small peptide structures (2LL5, 1D4P) as a short trajectory. Illustrates multi-frame playback.
Frames: 2LL5 → 1D4P (from RCSB PDB)
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)
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 inpublic/trajectories/or host elsewhere and use By file URL.
For single-structure viewing, see 3D Structure. Guide (reconstitution) · Peptide Library.