3D Protein Designer
Visualize, analyze, and edit protein structures in 3D. Powered by THREE.js with real-time rendering, Gaussian splatting surfaces, AI-powered structural analysis, and direct integration with the RCSB Protein Data Bank.
Key Features
Real-Time 3D Rendering
Powered by THREE.js with OrbitControls. Rotate, zoom, pan, and auto-rotate for full spatial exploration of molecular structures.
Multiple Representations
Three visualization modes: Cartoon (backbone trace with tubes), Sphere (space-filling atoms), and Stick (ball-and-stick with bonds).
Color Modes
Color by chain (distinct per peptide), by element (CPK standard colors), or by residue type (polar, non-polar, charged, aromatic).
RCSB PDB Integration
Search and fetch any structure from the Protein Data Bank by ID or keyword. Over 200,000 structures available at your fingertips.
Molecular Surface
Gaussian splatting renderer that projects atomic density onto a 2D surface. Additive blending with radial falloff for realistic electron cloud visualization.
Sequence Viewer
Amino acid sequence display with one-letter codes and residue-type colors. Click any residue to highlight it in the 3D view.
Mutation Tool
Select a residue by chain and sequence number, then mutate it to any of the 20 standard amino acids. See the structure update in real time.
AI-Powered Analysis
Every loaded structure is automatically analyzed by our LLM hub. Get insights about composition, secondary structure, and potential biological function.
High-Resolution Export
Export the current 3D view as a PNG screenshot or download the structure as a PDB file for offline use.
Multi-Chain Support
Visualize complex multi-chain proteins and protein complexes. Each chain is rendered with a distinct color for easy identification.
Visualization Modes
Cartoon
Backbone trace with tube geometry. Ideal for secondary structure visualization.
Sphere
Space-filling model. Each atom is a sphere with van der Waals radius.
Stick
Ball-and-stick with explicit bonds. Shows atomic connectivity.
How It Works
Search or Paste
Search the RCSB PDB by ID or keyword, or paste custom PDB data.
3D Visualization
Explore the structure with THREE.js. Switch representations and color modes.
Analyze & Edit
AI analyzes the structure. Use the mutation tool to modify residues.
Export & Share
Download as PDB or capture high-resolution screenshots.
Use Cases
Structural Biology Research
Visualize and analyze protein structures from RCSB PDB. Identify secondary structure elements, active sites, and domain architecture.
Drug Discovery
Examine binding pockets, visualize ligand interactions, and explore conformational states relevant to drug design.
Education & Teaching
Interactive molecular visualization for biochemistry and structural biology courses. Students can explore proteins in 3D without installing software.
Mutation Analysis
Predict the structural impact of amino acid substitutions. Useful for variant interpretation in personalized medicine.
Scientific Communication
Generate high-quality renders and screenshots for publications, presentations, and grant proposals.
Protein Engineering
Design and visualize engineered proteins. Explore the structural consequences of insertions, deletions, and substitutions.
Technology Stack
THREE.js
WebGL 3D rendering engine for real-time molecular visualization
RCSB PDB API
Direct integration with the Protein Data Bank for structure search and retrieval
Gaussian Splatting
2D projection of atomic electron density with additive blending
LLM Hub
AI-powered structural analysis using multi-provider language models
Explore Proteins in 3D
Search, visualize, and analyze any protein structure from the PDB.