proteinbench primary benchmark evidence

What this source contributed

Records in this release that cite this source. A record can cite several sources.

• 34 configurations
• 1 benchmark
• 96 tasks
• 6 dataset subsets
• 556 evaluations
• 556 results
• 107 evidence claims

Results

Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.

Claims

Statements this source supports, each with where in the source it was checked.

• ESM-IF1: family ESM-IF1: Family ESM-IF1 (Tables 2; task methods and corresponding named row)
• ESM3 (1.4B): family ESM3: Family ESM3 (Tables 4; task methods and corresponding named row)
• ESM3: family ESM3: Family ESM3 (Tables 2 and 5; task methods and corresponding named row)
• ESMFold: family ESMFold: Family ESMFold (Tables 7; task methods and corresponding named row)
• ESMFold: family ESMFold: Family ESMFold (Appendix B.2.3 Model implementations, ESMFold; Table7 CAMEO2022)
• OpenFold: family OpenFold: Family OpenFold (Tables 7; task methods and corresponding named row)
• ProteinBench AB-ACCURACY-AAR: part of discovery-benchmark-proteinbench: Part of ProteinBench (Table 6, column(Accuracy AAR ↑))
• ProteinBench AB-ACCURACY-RMSD: part of discovery-benchmark-proteinbench: Part of ProteinBench (Table 6, column(Accuracy RMSD ↓))
• ProteinBench AB-ACCURACY-TM-SCORE: part of discovery-benchmark-proteinbench: Part of ProteinBench (Table 6, column(Accuracy TM-score ↑))
• ProteinBench AB-FUNCTIONALITY-BINDING-ENERGY: part of discovery-benchmark-proteinbench: Part of ProteinBench (Table 6, column(Functionality Binding Energy ↓))
• ProteinBench AB-RATIONALITY-CLASHES-INNER: part of discovery-benchmark-proteinbench: Part of ProteinBench (Table 6, column(Rationality Clashes-inner ↓))
• ProteinBench AB-RATIONALITY-CLASHES-OUTER: part of discovery-benchmark-proteinbench: Part of ProteinBench (Table 6, column(Rationality Clashes-outer ↓))
• ProteinBench AB-RATIONALITY-CN-SCORE: part of discovery-benchmark-proteinbench: Part of ProteinBench (Table 6, column(Rationality CN-score ↑))
• ProteinBench AB-RATIONALITY-SCRMSD: part of discovery-benchmark-proteinbench: Part of ProteinBench (Table 6, column(Rationality scRMSD ↓))
• ProteinBench AB-RATIONALITY-SEQNAT: part of discovery-benchmark-proteinbench: Part of ProteinBench (Table 6, column(Rationality SeqNat ↑))
• ProteinBench AB-RATIONALITY-TOTAL-ENERGY: part of discovery-benchmark-proteinbench: Part of ProteinBench (Table 6, column(Rationality Total Energy ↓))
• ProteinBench AB-SPECIFICITY-PHR: part of discovery-benchmark-proteinbench: Part of ProteinBench (Table 6, column(Specificity PHR ↓))
• ProteinBench AB-SPECIFICITY-SEQSIM-INNER: part of discovery-benchmark-proteinbench: Part of ProteinBench (Table 6, column(Specificity SeqSim-inner ↑))
• ProteinBench AB-SPECIFICITY-SEQSIM-OUTER: part of discovery-benchmark-proteinbench: Part of ProteinBench (Table 6, column(Specificity SeqSim-outer ↓))
• ProteinBench against ProteinGym on ESM-IF1 and ProteinMPNN: different tasks: Discrepancy review explained (The outlier and consensus results of discrepancy-d734930095432234 as published at https://benchmarks.rewirebio.io/contested/discrepancy-d734930095432234/ (release 2026-10-23-968c8720eea6))
• ProteinBench against ProteinGym on ESM-IF1 and ProteinMPNN: different tasks: Discrepancy review explained (The outlier and consensus results of discrepancy-d734930095432234 as published at https://benchmarks.rewirebio.io/contested/discrepancy-d734930095432234/ (release 2026-10-23-968c8720eea6))
• ProteinBench against ProteinGym on ESM3 and ProteinMPNN: different tasks: Discrepancy review explained (The outlier and consensus results of discrepancy-f82ed80f71c6f0bd as published at https://benchmarks.rewirebio.io/contested/discrepancy-f82ed80f71c6f0bd/ (release 2026-10-23-968c8720eea6))
• ProteinBench against ProteinGym on ESM3 and ProteinMPNN: different tasks: Discrepancy review explained (The outlier and consensus results of discrepancy-f82ed80f71c6f0bd as published at https://benchmarks.rewirebio.io/contested/discrepancy-f82ed80f71c6f0bd/ (release 2026-10-23-968c8720eea6))
• ProteinBench BB-LENGTH-50-DIVERSITY-MAX-CLUST: part of discovery-benchmark-proteinbench: Part of ProteinBench (Table 3, column(length 50, Diversity Max Clust. ↑))
• ProteinBench BB-LENGTH-50-DIVERSITY-PAIRWISE-TM: part of discovery-benchmark-proteinbench: Part of ProteinBench (Table 3, column(length 50, Diversity pairwise TM ↓))

Models, benchmarks and other records

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.