A comprehensive PDB visualizer in VR
Beyond guided tours, NexoPeek is a full molecular visualization and analysis bench. Load any experimental structure or AI-predicted model, style it with one tap, isolate chains, measure atoms, predict pockets, and align structures — all at human scale, with bare hands or Quest controllers.
The 6-step workflow
Step 1
Source targets with smart search routing
Type a 4-character PDB ID for a direct RCSB download, or free text that cascades through full-text search, wildcard matching, UniProt gene lookup, and PDBe fallback. A validation checkpoint probes AlphaFold, SWISS-MODEL, and PDB concurrently so you never click a dead result.
Step 2
Publication-quality scenes in a single tap
Six native presets speak the MolViewSpec styling vocabulary: Cartoon + Ligand, Ball & Stick, Spacefill CPK, Cartoon + Pocket, Tube Trace, and B-Factor Heat. Stack independent overlays on top — hydrogen bonds, bond orders, electrostatic field lines, DX density isosurfaces, hydrophobicity.
Step 3
Isolate chains, residues, and waters
Scroll through polymer chains, ligands, and water molecules independently. Color-code chains to see interaction boundaries, tap residue pills to summon a white halo highlight in 3D space, and pin-point catalytic residues or active sites instantly.
Step 4
Interrogate with the spatial toolkit
Trigger-pick any two atoms for exact Angstrom distances with auto-labels. Scan hetero-compounds to isolate ligands and their hydrogen bonds. Summon cloud AI (PrankWeb/P2Rank) or the offline local engine to predict druggable pockets as tappable site chips, cross-referenced with UniProt catalytic sites.
Step 5
Compare via structural alignment
Load two structures and run Foldseek alignment over 3Di/AA encodings (with a local CE-style fallback) to compute a superposition matrix. Overlay binding-pocket geometries to compare domains — a critical first step in designing synthetic drug variants.
Step 6
Control the immersive environment
Slice cutplanes through active molecules to gaze inside binding channels. Capture XR-composite screenshots of exactly what your eyes see. Toggle Room View passthrough to float molecules in your physical room, or retreat to the void for deep focus — with automatic level-of-detail for smooth XR performance.
Scene presets
The presets speak the MolViewSpec styling vocabulary, mapped onto native on-device rendering for maximum XR performance — no state-tree interpreter needed.
Cartoon + Ligand
Sleek backbone cartoon with bound hetero-compounds highlighted.
Ball & Stick
Explicit atoms and bonds as spheres and cylinders.
Spacefill CPK
Full van der Waals radii in CPK colors for steric surfaces.
Cartoon + Pocket
Catalytic sites and binding pockets beside the main chain.
Tube Trace
Polymer backbone simplified to a smoothed tube.
B-Factor Heat
Temperature-factor gradient: flexibility vs rigidity.
Connected to the open scientific web
RCSB PDB & PDBe
Primary experimental structure retrieval
UniProt / InterPro
Curated catalytic sites, domains, annotations
AlphaFold & SWISS-MODEL
Predicted models at 95–99% accuracy
PrankWeb (P2Rank)
Cloud AI pocket prediction
Foldseek
Ultra-fast structural alignment
ChEMBL & PubChem
Bioactivity and ligand chemistry
The biotech discovery loop
1
Search & Procure
Translate curiosity into loaded spatial data via the open scientific web.
2
Style & Isolate
One-tap scenes, chain filtering, and residue spotlights.
3
Analyze & Measure
Extract hard data via distance picking and AI pocket mapping.
4
Learn & Hypothesize
Draw conclusions that spark the next search.