result · source checked
0.545 Top-1 ligand RMSD <2 Å rate
Boltz-1 · Top-1 ligand RMSD <2 Å rate · Boltz-1 structure test set
- Tested model
- Boltz-1
- Task or benchmark
- Protein–ligand pose prediction
- Dataset
- Boltz-1 structure test set
- Procedure
- Highest-confidence pose from five samples; precomputed MSAs up to 4,096 sequences.
- Evaluation
- Boltz-1: Protein–ligand pose prediction
- Evidence
- Author-reported evaluation · source checkedBoltz-1 Democratizing Biomolecular Interaction Modeling · Table 1, 3 recycling rounds / 200 steps row, L-RMSD <2Å top-1 column
A source-checked result verifies the numerical transcription, not every model or protocol detail. Evaluation metadata: needs review. Source checked does not mean independently reproduced.
Evaluation results
Release 2026-09-16-d74d282221a9 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| Boltz-1: Protein–ligand pose prediction Highest-confidence pose from five samples; precomputed MSAs up to 4,096 sequences. Author-reported evaluation · Evaluation metadata: needs review | ||
| 0.545 Top-1 ligand RMSD <2 Å rate Unit: unitless · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedBoltz-1 Democratizing Biomolecular Interaction Modeling · Table 1, 3 recycling rounds / 200 steps row, L-RMSD <2Å top-1 column Source checking is not independent reproduction. |
Sources and history
Release 2026-09-16-d74d282221a9 · Record review: source checked
- Boltz-1 Democratizing Biomolecular Interaction Modeling · Original source · PMC archival version PMC11601547.4
Technical metadata and extraction receipts
Stable ID: lit-b3-039
- areas
- molecular-interactions
- tasks
- Protein–ligand pose prediction
- printed value
- 0.545
- numeric value
- 0.545
- metric
- Top-1 ligand RMSD <2 Å rate
- metric direction
- unknown
- unit
- unitless
- uncertainty
- Not reported
- source locator
- Table 1, 3 recycling rounds / 200 steps row, L-RMSD <2Å top-1 column
- review
- method: independent_ai_table_review; reviewer: Codex omics research agent; independent source-table review, not human review; reviewed at: 2026-09-16T10:44:03.424864+00:00; notes: 3 recycling rounds and 200 steps; L-RMSD <2 Angstrom top-1 (last column), not oracle. Five samples generated; top-1 means highest-confidence candidate. Repeated reference rows are one evaluation, not independent experiments. Source check verifies central value and table context, not experiment reproduction or all metadata.; evidence: {"table_xml_id": "T4", "row_cells": ["3", "200", "0.729", "0.716", "0.654", "0.625", "0.621", "0.580", "0.581", "0.545"], "selected_cell_zero_based": 9, "selected_cell_xml": "<td align=\"center\" valign=\"top\" style=\"border-bottom: solid 1px\" rowspan=\"1\" colspan=\"1\">0.545</td>", "caption": "Ablation on the number of recycling rounds and sampling steps for Boltz-1 on the test set. We run the ablation study generating 5 samples and evaluating both the best (oracle) and highest confidence prediction (top-1) out of the 5 for every metric. All models used pre-computed MSAs with up to 4,096 sequences. It is worth noting that the metrics are noisy, so minor inconsistencies (e.g., lack of improvement with increased recycling rounds or diffusion steps) should not be overinterpreted. Moreover, there is a slight difference with the results in Figures 5 and 7 due to differences in MSA parameters as well as the set of structures passing all ablations."}; artifact sha256: 1ebf712314d9a1c678ded989cc95a0c00c0331e5ad8c9f63194bc9780971d214; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC11601547/fullTextXML
- legacy id
- lit-b3-039
- legacy row
- id: lit-b3-039; paper id: boltz1-2025; domain id: molecular-interactions; task: Protein–ligand pose prediction; model: Boltz-1; model version: 3 recycling rounds; 200 diffusion steps; dataset: Boltz-1 structure test set; dataset version: Not reported; split: Not reported; metric: Top-1 ligand RMSD <2 Å rate; value: 0.545; unit: unitless; uncertainty: Not reported; protocol: Highest-confidence pose from five samples; precomputed MSAs up to 4,096 sequences.; source locator: Table 1, 3 recycling rounds / 200 steps row, L-RMSD <2Å top-1 column; source url: https://pmc.ncbi.nlm.nih.gov/articles/PMC11601547/; evaluation origin: author_reported; reviewed utc: 2026-09-15T23:29:32Z
- missing metadata
- dataset version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract; uncertainty: not_reported_in_legacy_extract