Protein 3D Viewer
Protein 3D structure viewer (PDB / AlphaFold / ESMFold)
Tool Guide
Definition
Protein 3D Viewer — Fetches and renders protein 3D structures from PDB ID (experimental X-ray/Cryo-EM), AlphaFold UniProt accession (DeepMind AI prediction), or ESMFold input sequence (Meta AI single-sequence prediction). Interactive rotation/zoom via 3Dmol.js.
Purpose
(1) Visualize target protein domains and structural motifs (active sites, binding pockets) (2) Predict structure of novel sequences (no PDB) via ESMFold (~10 s) (3) Locate mutation sites (highlight key residues) (4) Foundation for antibody-antigen and drug binding-site modeling
How to Use
① Choose input mode: • PDB ID (e.g., 1CRN, 6VXX SARS-CoV-2 spike) • AlphaFold (UniProt accession, e.g., P12345) • ESMFold (amino acid sequence, ≤~400 aa recommended) ② Click "Load Structure" → 3D viewer renders ③ Interactions: • Mouse drag: rotate • Wheel: zoom • Style: cartoon / stick / sphere / surface • Color: spectrum (rainbow), chain, secondary structure ④ PNG export (screenshot) ESMFold uses Meta ESM Atlas API — ~10 s. Paste single sequence only (no FASTA header).
Examples
Example 1) SARS-CoV-2 Spike Protein → Input PDB ID: 6VXX → Trimer cartoon auto-renders → Inspect RBD region (319–541 aa) → visually validate vaccine target Example 2) Novel peptide sequence (no PDB) → ESMFold mode: "MVKVGVNGFGRIGRLVTRAAFNSGKVDIVAINDPFIDLNYMVYM..." → Structure renders in ~10 s (Rossmann fold visible)