| --- |
| license: cc-by-4.0 |
| tags: |
| - protein |
| - binder-design |
| - alphafold2 |
| - alphafold3 |
| configs: |
| - config_name: default |
| data_files: manifest.csv |
| --- |
| |
| # litscrape: AlphaFold2 + AlphaFold3 metrics |
|
|
| Per-design AlphaFold2 and AlphaFold3 confidence metrics for the binder–target |
| pairs in [`yk0/litscrape`](https://huggingface.co/datasets/yk0/litscrape). |
| The source dataset provides **sequences only** (no structures); these metrics |
| were produced by predicting/scoring each complex from sequence. |
|
|
| **4020 rows**, one per binder–target pair (4020 scored ok). |
|
|
| ## How the metrics were computed |
| 1. **Target structure** — each unique target *sequence* was folded once with |
| AF2 monomer (ColabDesign hallucination protocol) to obtain a target template. |
| 2. **AF2 metrics** (`af2_*`) — *de novo* AF2-Multimer (ColabDesign binder |
| protocol, single model `model_1_multimer_v3`, 3 recycles, no MSA, no initial |
| guess): the templated target + the binder *sequence* are folded into a |
| complex, and confidence metrics are read out. |
| 3. **AF3 metrics** (`af3_*`) — AF3Score run on the AF2-predicted complex, |
| conditioned on those coordinates (`init_guess=true`, no MSA). These are |
| AF3's confidence in the AF2 structure, **not** an independent de-novo AF3 |
| prediction. |
|
|
| ## Columns |
| - Metadata / labels carried over from the source dataset: binder_id, source_publication, target, label, binding_affinity_nm, target_sequence, binder_sequence |
| - `label` — binary experimental binding label (1 = binder, 0 = non-binder). |
| - AF2 (`model_1_multimer_v3`): af2_complex_plddt, af2_ptm, af2_iptm, af2_pae, af2_ipae, af2_min_ipae |
| (note: `af2_complex_plddt`/`af2_iptm` etc. are on a 0–1 scale; PAE values are |
| normalised as in ColabDesign). |
| - AF3: af3_ptm, af3_iptm, af3_chain_A_plddt, af3_chain_A_pae, af3_chain_A_ptm, af3_chain_A_iptm, af3_chain_B_plddt, af3_chain_B_pae, af3_chain_B_ptm, af3_chain_B_iptm, af3_iptm_A_B |
| (note: AF3 pLDDT is 0–100; `af3_chain_B_*` = binder chain; the per-chain |
| `iptm` fields equal `af3_iptm` for a 2-chain complex). |
| - `status`, `error`. |
| |
| ## Important caveats |
| - These are **de-novo predictions from sequence**, not refolds of designed |
| structures, so confidence values are markedly lower than initial-guess |
| pipelines (e.g. Proteina-Complexa evals) and are **not** directly comparable |
| to them in absolute terms. |
| - The target template is an AF2-*predicted* monomer, so target-fold error |
| propagates into every complex for that target. |
| - As classifiers of the experimental `label`, the metrics are weak-to-modest |
| (binder pLDDT is the most predictive; AUC ~0.60–0.68 on litscrape, lower on |
| proteinbase). AF3 closely tracks AF2 and adds little. |
|
|
