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AlphaFold 3 Server

VERIFIED

## Connections

structural-biology protein-complex deepmind

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

1. Go to https://alphafoldserver.com

2. Sign in with Google account

3. Enter protein sequences (FASTA format)

4. Add binding partners, DNA, RNA, ligands

5. Submit job (takes minutes to hours)

6. 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

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

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