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Protocol

Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding

Source-specific evaluation. Input conditions: co-folding. No equivalence to other releases, protocols or model families is inferred.

5 evaluations · 25 metric rows

Published comparisons

Each figure keeps its source, protocol, dataset and metric together. Results from different protocols are shown separately, without a pooled ranking.

Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding: protein_rmsd

protein_rmsd (angstrom) · Lower values are better for this metric.

Complete selected source table is retained across source-order panels. These point estimates do not establish statistical significance or a universal ranking.

Evaluation protocol · Plinder-L95

  1. AF3 · Configuration · Independent external evaluation0.3632
  2. Boltz-1 · Configuration · Independent external evaluation0.4041
  3. Boltz R1 · Configuration · Author-reported evaluation0.4056
  4. Boltz Rc · Configuration · Author-reported evaluation0.4068
  5. Boltz R · Configuration · Author-reported evaluation0.4102

Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.

Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a through Table 1 (XML tbl1); row Boltz R; column protein_rmsd; footnote a
Values, uncertainty and evidence
protein_rmsd: original source values
Tested entityPrinted valueUncertaintyEvidence
AF3 · Configuration0.3632 angstromNot reportedIndependent external evaluation · source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a
Boltz-1 · Configuration0.4041 angstromNot reportedIndependent external evaluation · source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz-1; column protein_rmsd; footnote a
Boltz R1 · Configuration0.4056 angstromNot reportedAuthor-reported evaluation · source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R1; column protein_rmsd; footnote a
Boltz Rc · Configuration0.4068 angstromNot reportedAuthor-reported evaluation · source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column protein_rmsd; footnote a
Boltz R · Configuration0.4102 angstromNot reportedAuthor-reported evaluation · source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R; column protein_rmsd; footnote a
Scope and limitations
  • Source-specific evaluation. Input conditions: co-folding. No equivalence to other releases, protocols or model families is inferred.
  • Exact source-defined evaluation scope; reported scores are not rewire reproductions.
  • Missing source cells and quarantined conflicts are recorded in acquisition and audit tables. Per-result scoring denominators may be unreported.

Source transcription and grouping reviewed by automated source review on 2026-09-19. These experiments were not independently reproduced by rewire.

Tested entities and results

Release 2026-09-19-eb6149e5d766 · 5 evaluations · 25 metric rows. Different protocols are not a single leaderboard. Charts retain each source table’s protocol and dataset.

Results grouped by the exact reported evaluation
Metric and findingCoverage and uncertaintyEvidence
Boltz-1 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95

Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries

Independent external evaluation · Evaluation metadata: discovered

60.58% chirality

Unit: percent · Direction: higher

Aggregation: percentage of molecules with consistent chirality

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz-1; column chirality; footnote a

Source checking is not independent reproduction.

0.0283 bond_rmsd

Unit: angstrom · Direction: lower

Aggregation: median

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz-1; column bond_rmsd; footnote a

Source checking is not independent reproduction.

0.4381 angle_rmsd

Unit: degree · Direction: lower

Aggregation: unreported in Table 1 footnote

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz-1; column angle_rmsd; footnote a

Source checking is not independent reproduction.

0.4041 protein_rmsd

Unit: angstrom · Direction: lower

Aggregation: median

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz-1; column protein_rmsd; footnote a

Source checking is not independent reproduction.

1.393 ligand_rmsd

Unit: angstrom · Direction: lower

Aggregation: median

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz-1; column ligand_rmsd; footnote a

Source checking is not independent reproduction.

Boltz Rc · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95

Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries

Author-reported evaluation · Evaluation metadata: discovered

0.2997 angle_rmsd

Unit: degree · Direction: lower

Aggregation: unreported in Table 1 footnote

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column angle_rmsd; footnote a

Source checking is not independent reproduction.

0.4068 protein_rmsd

Unit: angstrom · Direction: lower

Aggregation: median

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column protein_rmsd; footnote a

Source checking is not independent reproduction.

0.0215 bond_rmsd

Unit: angstrom · Direction: lower

Aggregation: median

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column bond_rmsd; footnote a

Source checking is not independent reproduction.

1.266 ligand_rmsd

Unit: angstrom · Direction: lower

Aggregation: median

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column ligand_rmsd; footnote a

Source checking is not independent reproduction.

100% chirality

Unit: percent · Direction: higher

Aggregation: percentage of molecules with consistent chirality

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz Rc; column chirality; footnote a

Source checking is not independent reproduction.

Boltz R1 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95

Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries

Author-reported evaluation · Evaluation metadata: discovered

99.77% chirality

Unit: percent · Direction: higher

Aggregation: percentage of molecules with consistent chirality

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R1; column chirality; footnote a

Source checking is not independent reproduction.

0.8973 angle_rmsd

Unit: degree · Direction: lower

Aggregation: unreported in Table 1 footnote

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R1; column angle_rmsd; footnote a

Source checking is not independent reproduction.

0.0345 bond_rmsd

Unit: angstrom · Direction: lower

Aggregation: median

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R1; column bond_rmsd; footnote a

Source checking is not independent reproduction.

0.4056 protein_rmsd

Unit: angstrom · Direction: lower

Aggregation: median

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R1; column protein_rmsd; footnote a

Source checking is not independent reproduction.

1.301 ligand_rmsd

Unit: angstrom · Direction: lower

Aggregation: median

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R1; column ligand_rmsd; footnote a

Source checking is not independent reproduction.

AF3 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95

Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries

Independent external evaluation · Evaluation metadata: discovered

0.1895 angle_rmsd

Unit: degree · Direction: lower

Aggregation: unreported in Table 1 footnote

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row AF3; column angle_rmsd; footnote a

Source checking is not independent reproduction.

0.9981 ligand_rmsd

Unit: angstrom · Direction: lower

Aggregation: median

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row AF3; column ligand_rmsd; footnote a

Source checking is not independent reproduction.

70.77% chirality

Unit: percent · Direction: higher

Aggregation: percentage of molecules with consistent chirality

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row AF3; column chirality; footnote a

Source checking is not independent reproduction.

0.3632 protein_rmsd

Unit: angstrom · Direction: lower

Aggregation: median

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a

Source checking is not independent reproduction.

0.0192 bond_rmsd

Unit: angstrom · Direction: lower

Aggregation: median

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row AF3; column bond_rmsd; footnote a

Source checking is not independent reproduction.

Boltz R · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95

Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries

Author-reported evaluation · Evaluation metadata: discovered

100% chirality

Unit: percent · Direction: higher

Aggregation: percentage of molecules with consistent chirality

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R; column chirality; footnote a

Source checking is not independent reproduction.

0.4102 protein_rmsd

Unit: angstrom · Direction: lower

Aggregation: median

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R; column protein_rmsd; footnote a

Source checking is not independent reproduction.

0.0448 angle_rmsd

Unit: degree · Direction: lower

Aggregation: unreported in Table 1 footnote

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R; column angle_rmsd; footnote a

Source checking is not independent reproduction.

0.0003 bond_rmsd

Unit: angstrom · Direction: lower

Aggregation: median

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R; column bond_rmsd; footnote a

Source checking is not independent reproduction.

1.381 ligand_rmsd

Unit: angstrom · Direction: lower

Aggregation: median

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1 (XML tbl1); row Boltz R; column ligand_rmsd; footnote a

Source checking is not independent reproduction.

Overview

Source-specific evaluation. Input conditions: co-folding. No equivalence to other releases, protocols or model families is inferred.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Benchmarks

These source-backed links do not make different protocols or scores interchangeable.

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-09-19-eb6149e5d766
Property and statementOriginal source and locationReview and provenance
Relationship: part of

discovery-benchmark-plinder

Individual claims
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction

Original source ↗

Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a

Version: version of record
Retrieved: 2026-09-16T10:41:16.555674+00:00

source checked

ai assisted source review · 2026-09-19

Audit details

Field: links:part_of:discovery-benchmark-plinder

Claim: acquired-membership-87c0192fa2f84a6f0441

Source artifact SHA-256: 78a77b9a0ab8bfa371f5b9baef3f443f4590d6e71cf864d67e90e9ebdfa7fc1b

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Sources and history

View linked audit checks and correction history

Release 2026-09-19-eb6149e5d766 · Record review: discovered

1 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: acquired-protocol-127e215c861a6b462f4d

source locator
Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a
procedure
Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries
comparison panels
id: acquired-figure-8094222acbebcc11b4f2; title: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding: protein_rmsd; protocol id: acquired-protocol-127e215c861a6b462f4d; dataset id: acquired-dataset-500bdf8d9750fb032041; metric: protein_rmsd; unit: angstrom; direction: lower; result ids: acquired-result-6faf6c42a6dd8edf0ac2; acquired-result-a4b3c4b66fe18cc9d21b; acquired-result-fce7e3c9c1d46ab98128; acquired-result-32f06faf32d402c4eda5; acquired-result-5263d447621b33ce5e5b; source ids: boltz-stereochemistry-2025; source locator: Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a through Table 1 (XML tbl1); row Boltz R; column protein_rmsd; footnote a; context: Complete selected source table is retained across source-order panels. These point estimates do not establish statistical significance or a universal ranking.; caveats: Source-specific evaluation. Input conditions: co-folding. No equivalence to other releases, protocols or model families is inferred.; Exact source-defined evaluation scope; reported scores are not rewire reproductions.; Missing source cells and quarantined conflicts are recorded in acquisition and audit tables. Per-result scoring denominators may be unreported.; review: method: automated_source_review; date: 2026-09-19; id: acquired-figure-984715eeec27c077427f; title: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding: ligand_rmsd; protocol id: acquired-protocol-127e215c861a6b462f4d; dataset id: acquired-dataset-500bdf8d9750fb032041; metric: ligand_rmsd; unit: angstrom; direction: lower; result ids: acquired-result-3ac1fef23b9aca0a889e; acquired-result-e39503fce61a297296ac; acquired-result-ff4210197bbd7b73b02c; acquired-result-c90ec06e22944401162b; acquired-result-c619fd03d1a8cff7d664; source ids: boltz-stereochemistry-2025; source locator: Table 1 (XML tbl1); row AF3; column ligand_rmsd; footnote a through Table 1 (XML tbl1); row Boltz R; column ligand_rmsd; footnote a; context: Complete selected source table is retained across source-order panels. These point estimates do not establish statistical significance or a universal ranking.; caveats: Source-specific evaluation. Input conditions: co-folding. No equivalence to other releases, protocols or model families is inferred.; Exact source-defined evaluation scope; reported scores are not rewire reproductions.; Missing source cells and quarantined conflicts are recorded in acquisition and audit tables. Per-result scoring denominators may be unreported.; review: method: automated_source_review; date: 2026-09-19; id: acquired-figure-026dd54449724728b3f6; title: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding: chirality; protocol id: acquired-protocol-127e215c861a6b462f4d; dataset id: acquired-dataset-500bdf8d9750fb032041; metric: chirality; unit: percent; direction: higher; result ids: acquired-result-560fed6d52eb275f657f; acquired-result-05806c3873a2f94389e5; acquired-result-0edddf6a1e99eb2289f2; acquired-result-e9a8c102cf9958f136c2; acquired-result-34733c1eac027089f71d; source ids: boltz-stereochemistry-2025; source locator: Table 1 (XML tbl1); row AF3; column chirality; footnote a through Table 1 (XML tbl1); row Boltz R; column chirality; footnote a; context: Complete selected source table is retained across source-order panels. These point estimates do not establish statistical significance or a universal ranking.; caveats: Source-specific evaluation. Input conditions: co-folding. No equivalence to other releases, protocols or model families is inferred.; Exact source-defined evaluation scope; reported scores are not rewire reproductions.; Missing source cells and quarantined conflicts are recorded in acquisition and audit tables. Per-result scoring denominators may be unreported.; review: method: automated_source_review; date: 2026-09-19; id: acquired-figure-54111c35cd4da8574346; title: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding: bond_rmsd; protocol id: acquired-protocol-127e215c861a6b462f4d; dataset id: acquired-dataset-500bdf8d9750fb032041; metric: bond_rmsd; unit: angstrom; direction: lower; result ids: acquired-result-e9442a7a5700ebd434a1; acquired-result-15f40069a96e46da45b8; acquired-result-c2577f7dbe1d94b392d2; acquired-result-9b8f4c327c80978893d8; acquired-result-650ab29b3de0ece95487; source ids: boltz-stereochemistry-2025; source locator: Table 1 (XML tbl1); row AF3; column bond_rmsd; footnote a through Table 1 (XML tbl1); row Boltz R; column bond_rmsd; footnote a; context: Complete selected source table is retained across source-order panels. These point estimates do not establish statistical significance or a universal ranking.; caveats: Source-specific evaluation. Input conditions: co-folding. No equivalence to other releases, protocols or model families is inferred.; Exact source-defined evaluation scope; reported scores are not rewire reproductions.; Missing source cells and quarantined conflicts are recorded in acquisition and audit tables. Per-result scoring denominators may be unreported.; review: method: automated_source_review; date: 2026-09-19; id: acquired-figure-1ffdfed8865d420ac29f; title: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding: angle_rmsd; protocol id: acquired-protocol-127e215c861a6b462f4d; dataset id: acquired-dataset-500bdf8d9750fb032041; metric: angle_rmsd; unit: degree; direction: lower; result ids: acquired-result-3043640ee3f9040d08cb; acquired-result-22c8b9360b643983347c; acquired-result-4b434a86debce56c5202; acquired-result-089b07d80b56536601c9; acquired-result-56da3028624a73810008; source ids: boltz-stereochemistry-2025; source locator: Table 1 (XML tbl1); row AF3; column angle_rmsd; footnote a through Table 1 (XML tbl1); row Boltz R; column angle_rmsd; footnote a; context: Complete selected source table is retained across source-order panels. These point estimates do not establish statistical significance or a universal ranking.; caveats: Source-specific evaluation. Input conditions: co-folding. No equivalence to other releases, protocols or model families is inferred.; Exact source-defined evaluation scope; reported scores are not rewire reproductions.; Missing source cells and quarantined conflicts are recorded in acquisition and audit tables. Per-result scoring denominators may be unreported.; review: method: automated_source_review; date: 2026-09-19
scope limitations
Exact source-defined evaluation scope; reported scores are not rewire reproductions.
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