AlphaFold 3

This package provides an implementation of the inference pipeline of AlphaFold 3. See below for how to access the model parameters. You may only use AlphaFold 3 model parameters if received directly from Google. Use is subject to these terms of use.

Any publication that discloses findings arising from using this source code, the model parameters or outputs produced by those should cite the Accurate structure prediction of biomolecular interactions with AlphaFold 3 paper.

Please also refer to the Supplementary Information for a detailed description of the method.

AlphaFold 3 is also available at alphafoldserver.com for non-commercial use, though with a more limited set of ligands and covalent modifications.

If you have any questions, please contact the AlphaFold team at alphafold@google.com.

Obtaining Model Parameters

This repository contains all necessary code for AlphaFold 3 inference. You can download the AlphaFold 3 model parameters from https://storage.googleapis.com/alphafold3/af3.bin.zst. Use is subject to these terms of use.

The models this fork runs

16 model types, and one --model flag decides which forward branches, config shapes, sampler constants and input conventions are used. The same input JSON drives all of them.

Two ENGINES live here. Everything in the first four groups rides the shared AlphaFold 3 graph — a pair+single trunk into a diffusion sampler — so adding one is a weight remap plus a branch. AlphaFold 2 shares neither end (MSA row/column attention, and an IPA head over backbone frames) and runs as a sibling network under alphafold3.af2, reached through the same CLI and the same output writer. Check model_registry.get(name).engine rather than testing the name.

AlphaFold 3 lineage

--model	model	weights
alphafold3	AlphaFold 3 (Google DeepMind)	request from DeepMind
openfold3	OpenFold3 preview-2 (AlQuraishi Lab)	Apache 2.0
openbind0	OpenFold3 v0.5.0 "OpenBind"	Apache 2.0
intellifold2	IntelliFold-v2 (IntelligenAI)	see upstream

Protenix family

Protenix publishes nine model types that differ only in counts and widths, so derive_dims + PROTENIX_FAMILY make each one close to a one-liner. This fork carried six of them and now runs two: protenix2, the flagship and the most completely gated model here, and protenix1. protenix05, protenix1_20250630, protenix_mini and protenix_tiny were removed on 2026-09-08 — they differed from these only by training run or by size, and keeping them spread parity work across variants without adding coverage. The machinery that made them one-liners is untouched, so re-adding one is still a sources.py entry, a converter alias and a MODELS line.

--model	model	weights
protenix2	Protenix-v2 (ByteDance)	Apache 2.0
protenix1	Protenix-v1	Apache 2.0

Other AF3-architecture models

--model	model	weights
boltz2	Boltz-2	MIT
opendde	OpenDDE (Aureka Research)	see upstream
rosettafold3	RoseTTAFold3 (RosettaCommons)	see upstream
chai1	chai-1 (Chai Discovery)	Apache 2.0

ESMFold2 family — folds from ESM-C, not an MSA

Pair-only trunk conditioned on an ESM-C language model.

--model	model	weights
esmfold2	ESMFold2 (Arc / CZ Biohub)	MIT
esmfold2_fast	ESMFold2-Fast — half the trunk	MIT
esmfold2_lm600m	…-base600M-step1500k — ESM-C 600M	MIT
esmfold2_lm300m	…-base300M-step1500k — ESM-C 300M	MIT

All but the last two condition on ESM-C 6B; those use the 600M and 300M towers and cost 0.5 GB and 0.3 GB against 5.1. Upstream ships the "Experimental" line for paper reproducibility rather than research use — its own card says to prefer plain esmfold2. The language-model input is built outside the fold by alphafold3.model.esm (tower, published int8 at 5.5 GB) plus a per-model shim that ships with the weights. Passing one variant another's tower reads corr 0.026 against native — take the pairing from model_registry.ESMFOLD2_VARIANTS[name]['esmc']. Given an MSA instead they fold from that: 5CAJ reads 17.5 Å from a single sequence and 1.24 Å at MSA depth 256. Supplying neither is the one broken configuration.

AlphaFold 2 — a sibling network, not the AF3 graph

--model	model	weights
af2_ptm	AlphaFold 2 monomer pTM (params_model_*_ptm.npz)	CC BY 4.0
af2_multimer	AlphaFold 2 multimer v3 (params_model_*_multimer_v3.npz)	CC BY 4.0

DeepMind's own AlphaFold 2 parameters, read from --model_dir as params/params_model_*.npz — nothing is converted or republished. Monomer and multimer run on ONE graph: a monomer checkpoint is converted onto the multimer network at load. Protein only — a fold input carrying a ligand, a nucleotide or an inter-chain bond raises rather than silently folding the protein subset. MSAs come from the AF3 data pipeline, chain pairing included, and the MSA pipeline is the model's own: subsampling, the cluster/extra split, BERT masking and clustering all run inside JAX under --seed, as they do upstream.

Templates work on both paths. A fold input carrying a template switches on the template embedder and the template-trained parameter sets — no flag, the input decides. Monomer templates exist only in model_1 and model_2 upstream, and only those two are used when templates are requested. Template residue types use AF2's restype alphabet, not the HHBLITS order the search tools emit; feeding the wrong one is silent and costs about 1.2 Å.

--num_recycles and --dropout reach AF2 exactly as they reach AF3.

AF2 is measured single-seed at float32 with zero recycles, not best-of-5 at config defaults like the AF3 lineage, so read the two AF2 numbers in Folds against each other rather than against the rest.

Parity status

This fork runs 16 model types, and the question for every one is whether it reproduces its own vendor's implementation rather than merely producing a plausible structure. PARITY.md is the full record and dev/oracles/HOLES.md tracks what is still open; this is the current state.

Parity is measured level by level, from the weights inwards to the fold:

level	what it compares
L0	conversion coverage — every checkpoint tensor accounted for, both directions
L1	the trunk: z-init, pairformer, MSA module, template embedder, distogram
L1r	the trunk on a REAL input: the input embedder, and recycling
L1x	the same, on a COMPLEX — the cross-chain terms are constant on one chain
L2	diffusion conditioning, token transformer, atom encoder and decoder
L3	one full denoise step
L4	the confidence head: PAE, PDE, pLDDT, resolved
L5	an end-to-end fold, scored against an experimental structure
L5af2	AlphaFold 2, module by module, against DeepMind's own repository
L6	modality: RNA, DNA, ligands, complexes, modified residues
L7	the OUTPUT side: fold, write the mmCIF, parse it back, compare
Lg	is the model differentiable in the sequence? (the design path)

Current numbers (2026-09-14)

Every level has been driven to completion across every model it applies to, L6 and L1x included. Grading each comparison on correlation and max|d|/rms:

369 cells                        295 OK   1 SKIP   73 N/A   0 FAIL
346 comparisons in 167 logs
PARITY=304   CLOSE=14   FLOOR=17   DIAG=6   LOOSE=5   BAD=0

The one SKIP is a real hole: boltz2 has no in-process L3 adapter, so its denoise step is gated by injection (L3.denoise_inject) instead.

DIAG is L1r and only L1r. Every other row compares one module on a bounded input, where corr >= 0.99999 is the right bar; L1r is the whole trunk on a real featurisation with ten recycles, where 48 blocks × 10 passes amplify and a correlation below 1.0 is normal even when the fold is right — 6MRR reads 0.991 on the pair while folding to 0.70 Å in agreement with native. It is read against its control case, not against a threshold. N/A means the model does not have that module at all — gate_applies.py decides, from the registry, so an empty cell can never quietly mean "not run".

AlphaFold 2 is graded separately, because none of L0-L4 applies to a sibling network with no converter and no shared modules. L5af2 is 18 gates, all green, and thirteen of them compare us to DeepMind's own repository rather than to the port we inherited — the trunk end to end, the structure module as a stack of eight fold iterations, extra-MSA, IPA, all five heads, all three template paths and the MSA pipeline, on the monomer path and the multimer path both. That oracle found three real divergences that comparing against a sibling copy never could: a masked template distogram, BERT masking that was implemented and never called (so the seed did nothing on a shallow MSA), and — on the AF3 side — a confidence pairformer that never received the dropout flag.

bash dev/oracles/run_all_parity.sh all re-runs everything; dev/oracles/parity_audit.py <logdir> grades it and dev/oracles/gate_applies.py <gate> <model> answers whether an empty cell is a hole or genuinely not applicable.

FLOOR is not a pass. It means the cell has no resolution left: perturbing the gate's own input by 1e-6 moves its output further than our port differs, so the number cannot be read. All 17 are the trunk pairformer on synthetic input, where the stack is driven far outside its trained distribution — the shallower L1.trunk1 is the measurement that counts. A cell only earns FLOOR by measuring it, so this cannot quietly excuse anything.

Nothing is BAD. The last cluster — 14 cells across the OpenFold3 lineage's atom encoder, decoder and denoise — was a regression introduced by a terminal-atom drop that MASKED atoms where the vendors REMOVE them, leaving a hole in the flat atom axis that shifted every attention window after it and left the dropped atom in the mmCIF to be written at the origin. Fixed on 2026-09-13; those cells went from 1.21 Å per-atom back to 0.0002.

The 5 LOOSE are all confidence tails — chai1's injected PAE/PDE logits, protenix2's PAE and PDE, opendde's PDE — every one at corr ≥ 0.99994 with a max|d|/rms of a few percent in the distribution's tail. esmfold2_fast's PAE and PDE, previously the 2 BAD, are understood the same way: native runs its confidence pairformer's triangle multiplications under autocast(bfloat16) while we run fp32, which costs ~0.5% per sub-module with bit-identical weights on identical inputs.

Folds

6MRR is best-of-5 CA-RMSD, de novo from a single sequence, 68 aa — the shared regression gate, and the L5 row of the matrix above. It says how well a model folds, not how faithfully it was ported; that is what L0-L4 measure.

model	best Å		model	best Å
boltz2	0.459		intellifold2	1.512
alphafold3	0.628		esmfold2_lm600m	1.522
opendde	0.729		openfold3	1.547
rosettafold3	0.967		protenix1	1.555
protenix2	1.016		openbind0	1.578
esmfold2_fast	1.182		esmfold2_lm300m	1.687
esmfold2	1.330		chai1	1.713

AlphaFold 2 runs single-seed at float32 with zero recycles rather than best-of-5, so its numbers belong beside each other and not in the table above: af2_ptm 1.712, af2_multimer 1.788.

Read these as a band, not a ranking. Several models are nondeterministic run to run on the same seed — three runs of rosettafold3 seed 0 give 0.968, 0.949 and 1.026, because one sample sits near a decision boundary — and best-of-5 is a TAIL statistic, so a single number to three decimals is not a gate. Two apparent regressions chased in 2026-09 were both one unlucky draw and dissolved at 20 samples. For a real comparison use means over ≥ 20 samples against native.

Modality

model	protein+ligand	complex	RNA	DNA	confidence
intellifold2	0.301 / 0.881	0.92	1.621	1.95	90.4 / r .776
boltz2	0.385 / 0.907	0.92	1.419	1.59	96.9 / r .830
protenix2	2.497 / 1.147	1.02	2.062	2.21	92.7 / r .807
rosettafold3	0.464 / 0.889	1.12	1.143	2.67	85.2 / r .708
opendde	1.269 / 0.870	1.49	1.372	1.99	89.9 / r .635
chai1	0.335 / 0.993	1.57	1.648	1.89	78.9 / r .543
openfold3	0.348 / 0.894	1.60	1.441	2.22	83.2 / r .678

r is the column that matters for confidence: a constant head reads r ≈ 0 however plausible its mean looks. All seven predict error. esmfold2_lm600m and esmfold2_lm300m ship no confidence head by design.

Every model is differentiable in the sequence — 16/16, both engines, the Lg level (dev/oracles/grad_check.py), which is what the design path needs. The 24/24 this line used to claim counted a model list that has since lost the four extra protenix variants; nothing ran the script, so nothing noticed.

What is still open

Tracked in dev/oracles/HOLES.md with the next measurement named for each:

• boltz2's denoise step, 0.207 Å/atom — closed 2026-09-13, and not by work aimed at it: the terminal-atom drop fix removed the atom instead of masking it, and the hole it had been leaving in the flat atom axis was what shifted every attention window. Now 0.0003 Å/atom at the highest-noise step and 0.0000 Å at the last one — both ends of the schedule are gated.
• the protenix lineage's confidence — attributed 2026-09-13, and not to what the last note guessed. It is torch.cdist: protenix feeds the raw distance to an unbinned linear, and cdist's float32 expansion of ||a-b||² costs up to 1.6e-02 Å on these coordinates. Give native an exact distance and all six CLOSE and three LOOSE rows collapse — protenix2 pae 2.30e-02 → 2.26e-04, opendde pde 1.58e-02 → 1.26e-04 — while openfold3, openbind0 and boltz2 are bit-unchanged. The earlier "native's own float32" story was tested directly (fp32 vs fp64 through the whole head) and is wrong by three orders.
• chai1's confidence, two LOOSE rows — now has a floor, which the previous note said was impossible: forward is undefined on the TorchScript archive but forward_256…forward_1024 are not, so native can be re-run. The head runs in bfloat16 with float32 geometry. Native against its own capture reads 1.62e-02 (pae) where our gate reads 4.73e-02 — 2–3× the cell's own resolution, so bounded rather than explained.
• three things no cell covers — closed 2026-09-13. L1b.msa_nonuniform reached one adapter of fourteen and duplicated the uniform cell for the rest; given a mask that is actually non-uniform the OpenFold3 lineage failed it (corr 0.9855, max|d|/rms 7.7) because of3 masks every transition's output and we did not. Fixed, and the membership of MASK_TRANSITIONS is now measured per model rather than inherited — though the divergence is dormant on our features, which was measured too. real_trunk_parity.py is now the L1r level: the input embedder, the trunk on a real featurisation, and recycling. boltz2's template V2 was closed on 2026-09-12 and the bullet was stale.
• AlphaFold 2 against DeepMind: the two whole-module cells are now built and green (native_trunk, native_structure); what remains is the monomer's TensorFlow row selection, which cannot be compared here (no tensorflow — we use multimer's gumbel argsort on both paths). Two deliberate differences, not unknowns: MSA sizes 512/1024 on both paths where stock is 512/5120 and 508/2048, and 11 trunk passes where of3/boltz2 run 4.

Getting the weights

You do not have to do anything. The first run of a model downloads its converted weights from huggingface.co/sokrypton/af3-any-model and caches them; every run after that is offline.

python run_alphafold.py \
  --model=openfold3 \
  --json_path=fold_input.json \
  --output_dir=./output/

They land in ~/.cache/alphafold3/weights/<model>/, or under $AF3_WEIGHTS_DIR if you set it. --model_dir overrides both and skips the download entirely, which is what you want for weights you converted or staged yourself. AlphaFold 3's own parameters are the exception: they are not ours to redistribute, so --model alphafold3 needs --model_dir pointing at your own copy.

Smaller downloads. --weights_precision int8 fetches the same weights stored as 8-bit with a per-channel scale, expanded back when the model loads. This is a storage format, not a compute one — inference is unchanged. Measured cost on rosettafold3: within sampling noise on protein, ligand, RNA and a D/L peptide, with stereochemistry unchanged.

fp16 is the same idea at half precision, and it now exists for every model — it had been an accepted flag with nothing published behind it, so --weights_precision fp16 was a 404 for all thirteen until 2026-09-16.

--model	fp32	fp16	int8
chai1	1.20 GB	0.60 GB	0.27 GB
protenix1	0.99 GB	0.47 GB	0.14 GB
protenix2	1.33 GB	0.61 GB	0.19 GB
rosettafold3	1.36 GB	0.65 GB	0.27 GB
openfold3	1.37 GB	0.68 GB	0.27 GB
openbind0	1.31 GB	0.68 GB	0.27 GB
intellifold2	1.77 GB	1.37 GB	0.63 GB
boltz2	1.88 GB	0.94 GB	0.36 GB
opendde	2.47 GB	0.94 GB	0.35 GB
esmfold2	0.87 GB	0.43 GB	0.18 GB

Each precision caches to its own directory (<model>-int8/), so asking for one never silently gets you the other, and switching back to a form you already have is instant.

Downloading the weights yourself

The repo is grouped by family and served over plain HTTPS, so nothing more than wget is needed — useful for pre-staging a shared filesystem or an air-gapped machine. A model's folder is its family, not its own name: the Protenix releases share protenix/, the eight ESMFold2 releases share esmfold2/, openbind0 sits with openfold3/, and the ESM2 and ESM-C towers are under lm/. The four Protenix model types this fork dropped on 2026-09-08 (protenix05, protenix1_20250630, protenix_mini, protenix_tiny) are still published under protenix/; they are simply no longer reachable through --model.

BASE=https://huggingface.co/sokrypton/af3-any-model/resolve/main
mkdir -p params/openfold3
wget -P params/openfold3 $BASE/openfold3/openfold3.bin.zst   # or .int8.bin.zst

python run_alphafold.py --model=openfold3 --model_dir=params/openfold3 ...

Locally a model keeps a flat directory named after itself; only the published layout is grouped. --model_dir therefore points at a directory holding <model>.bin.zst, exactly as before.

Or with the Hugging Face CLI:

pip install huggingface_hub
hf download sokrypton/af3-any-model openfold3/openfold3.bin.zst \
  --local-dir params

Converting the weights yourself

The published blobs are produced by converters/, and you can run it yourself against a checkpoint you already trust. Conversion needs PyTorch; a run never does.

# fetches the published checkpoint and converts it
python -m converters.convert --model openfold3 --out ./params/openfold3

Then run any model on the same input file:

python run_alphafold.py \
  --model=openfold3 \
  --model_dir=./params/openfold3 \
  --json_path=fold_input.json \
  --output_dir=./output/

chai-1 needs ESM2 embeddings

Two of the models fold from a protein language model, and are a different model without it: chai-1 from ESM2 3B, whose token embeddings are most of its token feature stream (a natural protein folds to 5.70 Å without them where chai reaches 0.642), and ESMFold2 from ESM-C, which is its alternative to an MSA rather than an extra on top of one (a variant with no MSA encoder folds to ~14 Å without it).

Both towers are converted and run here, in jax, so one flag covers both. Which tower is right is read from the model, not chosen on the command line — ESMFold2's variants are trained against step-matched ESM-C snapshots:

python run_alphafold.py --model=chai1         --use_esm_embeddings ...
python run_alphafold.py --model=esmfold2_fast --use_esm_embeddings ...

The tower runs in-process and is downloaded on demand (2.4 GB for ESM2, 5.1 GB for ESM-C 6B), which is why it is opt-in rather than the default. Running one of these models without the flag warns, because the result is a different model rather than a slightly worse one.

python -m alphafold3.model.esm also runs either tower standalone, if you want the hidden states themselves rather than a fold.

Cyclic chains

--cyclic=A,B (or --cyclic=all) makes those chains' relative-position encoding wrap, so they have no N- or C-terminus. This is not an AlphaFold 3 feature — the input JSON has no way to say it — but the encoding is shared, so every model here honours it. A chain left out is byte-identical to before.

The terms of use written beside a prediction follow the weights that made it, not AlphaFold 3's. See converters/README.md for what each conversion involves and OF3_AF3_PORTING_NOTES.md for the conventions that differ between these codebases and why.

Installation and Running Your First Prediction

See the installation documentation.

Once you have installed AlphaFold 3, you can test your setup using e.g. the following input JSON file named fold_input.json:

{
  "name": "2PV7",
  "sequences": [
    {
      "protein": {
        "id": ["A", "B"],
        "sequence": "GMRESYANENQFGFKTINSDIHKIVIVGGYGKLGGLFARYLRASGYPISILDREDWAVAESILANADVVIVSVPINLTLETIERLKPYLTENMLLADLTSVKREPLAKMLEVHTGAVLGLHPMFGADIASMAKQVVVRCDGRFPERYEWLLEQIQIWGAKIYQTNATEHDHNMTYIQALRHFSTFANGLHLSKQPINLANLLALSSPIYRLELAMIGRLFAQDAELYADIIMDKSENLAVIETLKQTYDEALTFFENNDRQGFIDAFHKVRDWFGDYSEQFLKESRQLLQQANDLKQG"
      }
    }
  ],
  "modelSeeds": [1],
  "dialect": "alphafold3",
  "version": 1
}

You can then run AlphaFold 3 using the following command:

docker run -it \
    --volume $HOME/af_input:/root/af_input \
    --volume $HOME/af_output:/root/af_output \
    --volume <MODEL_PARAMETERS_DIR>:/root/models \
    --volume <DATABASES_DIR>:/root/public_databases \
    --gpus all \
    alphafold3 \
    python run_alphafold.py \
    --json_path=/root/af_input/fold_input.json \
    --model_dir=/root/models \
    --output_dir=/root/af_output

There are various flags that you can pass to the run_alphafold.py command, to list them all run python run_alphafold.py --help. Two fundamental flags that control which parts AlphaFold 3 will run are:

• --run_data_pipeline (defaults to true): whether to run the data pipeline, i.e. genetic and template search. This part is CPU-only, time consuming and could be run on a machine without a GPU.
• --run_inference (defaults to true): whether to run the inference. This part requires a GPU.

AlphaFold 3 Input

See the input documentation.

AlphaFold 3 Output

See the output documentation.

Performance

See the performance documentation.

Known Issues

Known issues are documented in the known issues documentation.

Please create an issue if it is not already listed in Known Issues or in the issues tracker.

Citing This Work

Any publication that discloses findings arising from using this source code, the model parameters or outputs produced by those should cite:

@article{Abramson2024,
  author  = {Abramson, Josh and Adler, Jonas and Dunger, Jack and Evans, Richard and Green, Tim and Pritzel, Alexander and Ronneberger, Olaf and Willmore, Lindsay and Ballard, Andrew J. and Bambrick, Joshua and Bodenstein, Sebastian W. and Evans, David A. and Hung, Chia-Chun and O’Neill, Michael and Reiman, David and Tunyasuvunakool, Kathryn and Wu, Zachary and Žemgulytė, Akvilė and Arvaniti, Eirini and Beattie, Charles and Bertolli, Ottavia and Bridgland, Alex and Cherepanov, Alexey and Congreve, Miles and Cowen-Rivers, Alexander I. and Cowie, Andrew and Figurnov, Michael and Fuchs, Fabian B. and Gladman, Hannah and Jain, Rishub and Khan, Yousuf A. and Low, Caroline M. R. and Perlin, Kuba and Potapenko, Anna and Savy, Pascal and Singh, Sukhdeep and Stecula, Adrian and Thillaisundaram, Ashok and Tong, Catherine and Yakneen, Sergei and Zhong, Ellen D. and Zielinski, Michal and Žídek, Augustin and Bapst, Victor and Kohli, Pushmeet and Jaderberg, Max and Hassabis, Demis and Jumper, John M.},
  journal = {Nature},
  title   = {Accurate structure prediction of biomolecular interactions with AlphaFold 3},
  year    = {2024},
  volume  = {630},
  number  = {8016},
  pages   = {493–-500},
  doi     = {10.1038/s41586-024-07487-w}
}

Acknowledgements

AlphaFold 3's release was made possible by the invaluable contributions of the following people:

Andrew Cowie, Bella Hansen, Charlie Beattie, Chris Jones, Grace Margand, Jacob Kelly, James Spencer, Josh Abramson, Kathryn Tunyasuvunakool, Kuba Perlin, Lindsay Willmore, Max Bileschi, Molly Beck, Oleg Kovalevskiy, Sebastian Bodenstein, Sukhdeep Singh, Tim Green, Toby Sargeant, Uchechi Okereke, Yotam Doron, and Augustin Žídek (engineering lead).

We also extend our gratitude to our collaborators at Google and Isomorphic Labs.

AlphaFold 3 uses the following separate libraries and packages:

• abseil-cpp and abseil-py
• Docker
• DSSP
• HMMER Suite
• Haiku
• JAX
• libcifpp
• NumPy
• pybind11 and pybind11_abseil
• RDKit
• Tokamax
• tqdm

We thank all their contributors and maintainers!

Running other models through this code

Everything under The models this fork runs rests on work by other people. First and most obviously the model authors, who trained and released the weights — each is linked in that table, and each should be cited alongside AlphaFold 3 if you use their model.

Beyond them, three whose code this borrows from directly:

• Marielle Russo — plegadx, an Equinox/JAX re-implementation of RoseTTAFold3, Boltz, chai-1, IntelliFold and AlphaFold 3 on a shared substrate, each validated against its vendor implementation. Its chai-1 diffusion modules were the op-level reference while ours was being debugged, and its sampler — replayed to 0.00015 Å under identical noise — independently confirmed two details we had derived separately: that the vendor loop runs len(sigmas) - 1 iterations, and that it augments with a rotation and a translation each step. Its chai-1 trunk diverged in the same place ours did, which is its own kind of signpost.

• ChoongHwanLee — an independent Protenix → AlphaFold 3 port (ColabFold, colabfold2-protenix-proof), built on this same Haiku graph. Two things here come straight from it. One is the padded-key attention mask, which protenix2 and opendde were missing. The other is the discipline of asserting that every checkpoint tensor is consumed exactly once — dev/audit_coverage.py is that check (dev-only, out of tree), and it found four dropped distogram biases, three LayerNorm offsets and a single-conditioner bias that eight ports' worth of correlation gates had all scored as passing. Independent agreement on the rest of the Protenix config is the strongest evidence either port has.

• juliabuhmann — the OpenBind port (PR #6). She found that OpenFold3's v0.5.0 weights revert two of the deviations this code compensates for, worked out which, and built the one-key checkpoint detection that tells the two releases apart without a version string. --model openbind0 is her work, re-expressed for this branch's per-model registry.

• Milot Mirdita — ColabFold and the public MMseqs2 API. src/alphafold3/data/msa_server.py is adapted from ColabFold's run_mmseqs2, which is what lets this run with no local sequence database at all. The device-portability matrix in run_alphafold.py — which attention implementation and which XLA flags each GPU generation needs — also comes from ColabFold, where every row of it was paid for by a real failure.

Get in Touch

If you have any questions not covered in this overview, please contact the AlphaFold team at alphafold@google.com.

We would love to hear your feedback and understand how AlphaFold 3 has been useful in your research. Share your stories with us at alphafold@google.com.

Licence and Disclaimer

This is not an officially supported Google product.

Copyright 2024 DeepMind Technologies Limited.

AlphaFold 3 Source Code and Model Parameters

AlphaFold 3 source code is licensed under the Apache License, Version 2.0 (the "License"); you may not use its source code except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0.

The AlphaFold 3 model parameters are made available under the AlphaFold 3 Model Parameters Terms of Use (the "Terms"); you may not use these except in compliance with the Terms. You may obtain a copy of the Terms at https://github.com/google-deepmind/alphafold3/blob/main/WEIGHTS_TERMS_OF_USE.md.

Unless required by applicable law, AlphaFold 3 and its output are distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. You are solely responsible for determining the appropriateness of using AlphaFold 3, or using or distributing its source code or output, and assume any and all risks associated with such use or distribution and your exercise of rights and obligations under the relevant terms. Output are predictions with varying levels of confidence and should be interpreted carefully. Use discretion before relying on, publishing, downloading or otherwise using the AlphaFold 3 Assets.

AlphaFold 3 and its output are for theoretical modeling only. They are not intended, validated, or approved for clinical use. You should not use the AlphaFold 3 or its output for clinical purposes or rely on them for medical or other professional advice. Any content regarding those topics is provided for informational purposes only and is not a substitute for advice from a qualified professional. See the relevant terms for the specific language governing permissions and limitations under the terms.

Third-party Software

Use of the third-party software, libraries or code referred to in the Acknowledgements section above may be governed by separate terms and conditions or license provisions. Your use of the third-party software, libraries or code is subject to any such terms and you should check that you can comply with any applicable restrictions or terms and conditions before use.

Mirrored and Reference Databases

The following databases have been: (1) mirrored by Google DeepMind; and (2) in part, included with the inference code package for testing purposes, and are available with reference to the following:

• BFD (modified), by Steinegger M. and Söding J., modified by Google DeepMind, available under a Creative Commons Attribution 4.0 International License. See the Methods section of the AlphaFold proteome paper for details.
• PDB (unmodified), by H.M. Berman et al., available free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use under CC0 1.0 Universal (CC0 1.0) Public Domain Dedication.
• MGnify: v2022_05 (unmodified), by Mitchell AL et al., available free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use under CC0 1.0 Universal (CC0 1.0) Public Domain Dedication.
• UniProt: 2021_04 (unmodified), by The UniProt Consortium, available under a Creative Commons Attribution 4.0 International License.
• UniRef90: 2022_05 (unmodified) by The UniProt Consortium, available under a Creative Commons Attribution 4.0 International License.
• NT: 2023_02_23 (modified) See the Supplementary Information of the AlphaFold 3 paper for details.
• RFam: 14_4 (modified), by I. Kalvari et al., available free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use under CC0 1.0 Universal (CC0 1.0) Public Domain Dedication. See the Supplementary Information of the AlphaFold 3 paper for details.
• RNACentral: 21_0 (modified), by The RNAcentral Consortium available free of all copyright restrictions and made fully and freely available for both non-commercial and commercial use under CC0 1.0 Universal (CC0 1.0) Public Domain Dedication. See the Supplementary Information of the AlphaFold 3 paper for details.