AlphaFold 3 Server
Google DeepMind’s latest protein structure prediction system. Predicts complexes of proteins, DNA, RNA, and small molecules — not just single chains.
What It Does
- Predicts 3D structures of protein complexes (protein-protein, protein-DNA, protein-ligand)
- Confidence metrics: pTM (overall), ipTM (interface), pLDDT (per-residue)
- Supports custom sequences (mutants, truncations)
- Up to 5,000 residues per job
How to Use
Web Interface
- Go to https://alphafoldserver.com
- Sign in with Google account
- Enter protein sequences (FASTA format)
- Add binding partners, DNA, RNA, ligands
- Submit job (takes minutes to hours)
- Download results (PDB + confidence JSON)
Job Submission Tips
- Name jobs clearly: “STRC_E1659A_TMEM145_complex”
- For mutants: modify the amino acid in the sequence directly
- For truncations: paste only the fragment sequence
- Run wild-type AND mutant side by side for comparison
Verified Status
VERIFIED — 16 STRC experiments run. Key results: WT pTM 0.63, E1659A pTM 0.64 (structure intact), mini-STRC retains TMEM145 binding (ipTM 0.43 vs 0.47 full-length).
STRC Research Usage
- STRC AlphaFold3 Computational Experiments — 16 systematic experiments
- STRC AF3 Truncation Boundary Sweep — identified optimal mini-STRC boundaries
- STRC Mini-STRC Single-Vector Hypothesis — validated that truncated STRC binds TMEM145
- STRC Electrostatic Analysis E1659A — showed E1659A folds normally but loses charge
Key Results Archive
| Experiment | pTM | ipTM | Finding |
|---|---|---|---|
| Full STRC WT | 0.63 | — | Baseline structure |
| Full STRC E1659A | 0.64 | — | Structure-function paradox confirmed |
| Mini-STRC (616-1775) + TMEM145 | — | 0.43 | Binding retained |
| Full STRC + TMEM145 | — | 0.47 | Reference binding |
| Mini-STRC (700-1775) + TMEM145 | — | 0.43 | Also works |
| Mini-STRC (700-1780) + TMEM145 | — | 0.91 | Best binding — includes GPI anchor signal |
Next Steps
- STRC + cochlin/otogelin — predict interactions with other stereocilia proteins
- STRC + lipid bilayer — model GPI-anchor attachment
- Drug screening — test small molecule binding to E1659 pocket
- Saturation mutagenesis done computationally via AlphaMissense (all 19 subs pathogenic), AF3 structural comparison would add 3D dimension
Connections
- AlphaFold Database [see-also] — single-chain predictions
- STRC AlphaFold3 Computational Experiments [used-in]
- STRC Mini-STRC Single-Vector Hypothesis [used-in]
- STRC Electrostatic Analysis E1659A [used-in]
- AlphaMissense [see-also] — pathogenicity scores