Pith Number

pith:YXRUPWHI

pith:2026:YXRUPWHI7D2CLCZU3G7BBD3ZAL

not attested not anchored not stored refs pending

ProtDBench: A Unified Benchmark of Protein Binder Design and Evaluation

Chengyue Gong, Cong Liu, Jiaqi Guan, Jinyuan Sun, Milong Ren, Wenzhi Xiao, Xinshi Chen

A new benchmark for protein binder design shows that common structure prediction models disagree substantially on which designs succeed under identical rules.

arxiv:2605.04118 v2 · 2026-05-05 · q-bio.QM · cs.AI

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\usepackage{pith}
\pithnumber{YXRUPWHI7D2CLCZU3G7BBD3ZAL}

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Record completeness

1 Bitcoin timestamp

2 Internet Archive

3 Author claim open · sign in to claim

4 Citations open

5 Replications open

✓ Portable graph bundle live · download bundle · merged state

The bundle contains the canonical record plus signed events. A mirror can host it anywhere and recompute the same current state with the deterministic merge algorithm.

Claims

C1strongest claim

Using a large wet-lab annotated dataset, we analyze commonly used structure prediction models as evaluation verifiers, revealing substantial verifier-dependent bias and limited agreement under identical filtering protocols. ... Overall, ProtDBench provides a fair and reproducible evaluation pipeline that supports systematic and controlled comparison of protein binder design methods under realistic evaluation settings.

C2weakest assumption

That the defined success criteria, filtering protocols, and wet-lab annotated dataset accurately reflect real experimental binder performance and provide a representative basis for benchmarking.

C3one line summary

ProtDBench standardizes protein binder design evaluation using wet-lab data, exposing verifier biases, metric dependencies, and trade-offs between success rate, speed, and structural diversity.

Formal links

3 machine-checked theorem links

Receipt and verification

First computed	2026-05-25T02:02:16.241048Z
Builder	pith-number-builder-2026-05-17-v1
Signature	Pith Ed25519 (`pith-v1-2026-05`) · public key
Schema	pith-number/v1.0

Canonical hash

c5e347d8e8f8f4258b34d9be108f7902c3754fa0392a20e7f11152d771719371

Aliases

arxiv: 2605.04118 · arxiv_version: 2605.04118v2 · doi: 10.48550/arxiv.2605.04118 · pith_short_12: YXRUPWHI7D2C · pith_short_16: YXRUPWHI7D2CLCZU · pith_short_8: YXRUPWHI

Agent API

Resolver JSON Graph JSON Events JSON Schema Signing key

Verify this Pith Number yourself

curl -sH 'Accept: application/ld+json' https://pith.science/pith/YXRUPWHI7D2CLCZU3G7BBD3ZAL \
  | jq -c '.canonical_record' \
  | python3 -c "import sys,json,hashlib; b=json.dumps(json.loads(sys.stdin.read()), sort_keys=True, separators=(',',':'), ensure_ascii=False).encode(); print(hashlib.sha256(b).hexdigest())"
# expect: c5e347d8e8f8f4258b34d9be108f7902c3754fa0392a20e7f11152d771719371

Canonical record JSON

{
  "metadata": {
    "abstract_canon_sha256": "9bc5302669094ee96b4db6b9698023741e2216b324eb8f9eafe8add32dfaabc2",
    "cross_cats_sorted": [
      "cs.AI"
    ],
    "license": "http://arxiv.org/licenses/nonexclusive-distrib/1.0/",
    "primary_cat": "q-bio.QM",
    "submitted_at": "2026-05-05T11:48:59Z",
    "title_canon_sha256": "29ff778fc392f8d1cc0d4cccd4cc6a6ff4f34f38282127e94d7386357ab61d32"
  },
  "schema_version": "1.0",
  "source": {
    "id": "2605.04118",
    "kind": "arxiv",
    "version": 2
  }
}