Result

Ligand RMSD under 2a rate (top-1 pose; binding-site superposition (OpenStructure 2.8); averaged per complex; atom set not stated) of Boltz-1 on Boltz-1 structure test set

0.545 Ligand RMSD under 2a rate (top-1 pose; binding-site superposition (OpenStructure 2.8); averaged per complex; atom set not stated)

Methods

Tested configuration: Boltz-1
Task: Protein–ligand pose prediction
Dataset: Boltz-1 structure test set
Related family profiles: Boltz
Procedure: Highest-confidence pose from five samples; precomputed MSAs up to 4,096 sequences.
Evaluation: Boltz-1: Protein–ligand pose prediction
Coverage: Not reported scored / Not reported eligible
Uncertainty: Not yet extracted
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.

Reproduction

Split: Not reported
Adaptation: Not reported
Scoring implementation: Not reported

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Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

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

Evidence table

Inspect claims, sources and review details

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1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statement	Original source and location	Review and provenance
Printed value 0.545 Individual claims	Boltz-1 Democratizing Biomolecular Interaction Modeling Original source ↗ Table 1, 3 recycling rounds / 200 steps row, L-RMSD <2Å top-1 column Version: PMC archival version PMC11601547.4 Retrieved: 2026-09-16T10:44:03.424864+00:00	source checked ["ai-assisted-source-review"] · 2026-09-16T10:44:03.424864+00:00 author reported Audit details 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. Field: `attributes.printed_value` Claim: claim-lit-b3-039 Source artifact SHA-256: `1ebf712314d9a1c678ded989cc95a0c00c0331e5ad8c9f63194bc9780971d214` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact Extraction artifact SHA-256: `1ebf712314d9a1c678ded989cc95a0c00c0331e5ad8c9f63194bc9780971d214` Extraction artifact

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Sources and history

Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

1 source record and release history

Boltz-1 Democratizing Biomolecular Interaction Modeling · Original source · PMC archival version PMC11601547.4

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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: ligand-rmsd-under-2a-rate
metric direction: unknown
unit: fraction
source locator: Table 1, 3 recycling rounds / 200 steps row, L-RMSD <2Å top-1 column
review: method: ai-assisted-source-review; reviewer: codex; reviewed at: 2026-09-16T10:44:03.424864+00:00; 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; method note: independent; table-level review; reviewer note: role: omics research agent; independent source-table review; not human review; note: 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.
legacy id: lit-b3-039
missing metadata: dataset version: reason: unextracted; split: reason: unextracted; uncertainty: reason: unextracted
metric qualifier: top-1 pose; binding-site superposition (OpenStructure 2.8); averaged per complex; atom set not stated

Related records

evaluation: Boltz-1: Protein–ligand pose prediction
subject: Reported Top-1 ligand RMSD <2 Å rate for Boltz-1

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