| --- |
| tags: |
| - protein-structure-prediction |
| - alphafold3 |
| - deepfold3 |
| --- |
| |
| # DeepFold3 |
|
|
| Weights for DeepFold3, a PyTorch biomolecular complex structure predictor architecturally equivalent to AlphaFold 3. |
| Each `.safetensors` file embeds its architectural `ModelConfig` as JSON in the header (`model_cfg_json`), so |
| `deepfold3 inference` rebuilds the trained architecture without a sidecar config. |
|
|
| ## Checkpoints |
|
|
| | File | Run | Step | Snapshot | Params | SHA-256 | |
| | --- | --- | --- | --- | --- | --- | |
| | `df3-stage1-r19/checkpoint_120000.safetensors` | df3-stage1-r19 | 120,000 | EMA shadow (decay 0.999) | 310,190,170 (fp32) | `aef0468336c0a0ed7ecdadbb5397cfbfe3de0c552b72957dc77b6d1fea29ba2e` | |
|
|
| ## df3-stage1-r19 @ 120k |
|
|
| **Architecture (r19).** The trunk has no triangle attention and no single track: each PairFormer block is |
| TriMulOutgoing + TriMulIncoming (plain AF3 TriangleMul) + FFN. Diffusion conditioning does not consume the trunk single (`conditioning_use_trunk_single: false`). |
| The confidence-head and template PairFormers are unchanged from AF3. |
|
|
| | | | |
| | --- | --- | |
| | pair / single / MSA channels | 256 / 384 / 128 | |
| | PairFormer layers | 48 | |
| | MSA module layers | 4 | |
| | Diffusion transformer blocks | 24 | |
| | Confidence PairFormer layers | 4 | |
| | Recycles | 10 | |
|
|
| **Training.** |
|
|
| - Stage 0 from scratch (`configs/df3-stage0-r19.yaml`) to step 71,000, then stage 1 (`configs/stage1.yaml`: |
| 512-token crop, bond loss on, shape-complementarity loss 0.03) resumed from that checkpoint. |
| - AdamW, lr 9e-4, EMA decay 0.999, 112 GPUs. |
| - Dataset mix (weights at step 120k): OpenFold3 `pdb_training_set` 0.5, OF3 long monomers 0.2, AFDB (NVIDIA) |
| 0.15, TEDdymer 0.1, OF3 short monomers 0.05. The weighted PDB set was `patchr` until step 20,000. |
| - Step 120,000 is the optimizer step (`effective_step`). The checkpoint's `global_step` is 169,000 because stage 1 |
| accumulates 2 micro-batches per step. |
|
|
| **Export.** `deepfold3 export --snapshot auto` from `runs/df3-stage1-r19/checkpoint_120000.pt` (commit `131baf6`). |
| The run is AdamW + EMA, so `auto` selects the EMA shadow (the deployment snapshot used by inference and eval). |
| Verified bitwise-identical to the checkpoint's shadow overlay; loads into `DeepFold3` with no missing or |
| unexpected keys. |
|
|
| ## Usage |
|
|
| ```bash |
| hf download vv137/deepfold3 df3-stage1-r19/checkpoint_120000.safetensors --local-dir weights/ |
| deepfold3 inference --json input.json --output out/ \ |
| --params weights/df3-stage1-r19/checkpoint_120000.safetensors |
| ``` |
|
|
