AlphaFold 3 3
Diffusion-based successor that predicts joint structures of proteins with DNA, RNA, ligands, ions and modified residues — the interaction types that matter for drug design and for understanding oncogenic complexes.
At a glance
What it does
Models complexes (protein–ligand, protein–nucleic acid, antibody–antigen) in one network; AlphaFold Server offers free non-commercial predictions, and the code and weights (on request) allow local runs.
Tasks, data types and cancers
Architecture
Training data
Protein Data Bank complexes including ligands and nucleic acids (cut-off 2021), with distillation data as in AlphaFold 2.
Linked datasets
- training Protein Data Bank (wwPDB / RCSB) Open download
Evaluation
| Benchmark / dataset | Metric | Value | External validation | Source |
|---|---|---|---|---|
| PoseBusters (protein–ligand) | % poses within 2 Å RMSD | substantially above docking baselines (paper) | yes | Source |
How to run
Model parameters are granted for academic use on request (form linked from the repo); commercial use requires a licence from Isomorphic Labs. The Server is the zero-setup route.
Regulatory status and intended use
Regulatory status is quoted from the source linked above and can change. Research-use-only models must not be used for clinical decisions.
Limitations and bias
- Hallucinated structure in disordered regions; occasional chirality/clash errors flagged by the confidence outputs.
- Non-commercial weights; commercial drug-discovery use is licensed separately.
Sources
This page is educational — it is not medical advice and does not replace consultation with an oncologist. Diagnostic and treatment decisions are made solely by specialist physicians.