AF3 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95
Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries; Plinder-L95. Source checked, not independently reproduced.
Evaluation results
Release 2026-09-19-eb6149e5d766 · 1 evaluation · 5 metric rows. Different protocols are not a single leaderboard. Charts retain each source table’s protocol and dataset.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| AF3 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 Configuration: AF3Protocol: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-foldingDataset subset: 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. |
Methods and reproduction
Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries; Plinder-L95. Source checked, not independently reproduced.
- configuration
- AF3
- protocol
- Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding
- dataset subset
- Plinder-L95
- Split
- all entries (includes Before and After training cutoff subsets)
- Adaptation
- unreported
- Scoring implementation
- Not reported
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
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.
Evaluation procedure
Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries
- Configuration
- AF3
- Protocol
- Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding
- Dataset subset
- Plinder-L95
- origin
- Independent external evaluation
- configuration
- Not reported
- protocol id
- acquired-protocol-127e215c861a6b462f4d
- dataset version
- ACS Omega 2025 version of record; PMC12658688 XML retrieved 2026-09-19
- split
- all entries (includes Before and After training cutoff subsets)
- population
- Plinder-L95
- inputs
- co-folding
- adaptation
- unreported
- aggregation
- metric-specific; inspect each result
Metadata review: discovered. Unreported conditions prevent automatic comparisons.
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.
26 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.comparison.adaptation unreported Context-only references | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a Version: version of record | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.aggregation metric-specific; inspect each result Context-only references | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a Version: version of record | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.dataset_version ACS Omega 2025 version of record; PMC12658688 XML retrieved 2026-09-19 Context-only references | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a Version: version of record | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.inputs co-folding Context-only references | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a Version: version of record | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.population Plinder-L95 Context-only references | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a Version: version of record | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.protocol_id acquired-protocol-127e215c861a6b462f4d Context-only references | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a Version: version of record | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.split all entries (includes Before and After training cutoff subsets) Context-only references | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a Version: version of record | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.conditions.checkpoint_hash No value recorded Context-only references | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a Version: version of record | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.conditions.comparison_compatibility mixed_input_information; descriptive source table only, no ranked fair-comparison claim Context-only references | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a Version: version of record | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.conditions.dataset_size 6600 Context-only references | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a Version: version of record | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
Release 2026-09-19-eb6149e5d766 · Record review: discovered
1 source records and release history
- Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Original source · version of record
Technical metadata and extraction receipts
Stable ID: acquired-evaluation-b58708621b68a98da3ab
- origin
- independent_paper
- protocol
- Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries
- source locator
- Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a
- conditions
- checkpoint hash: Not reported; comparison compatibility: mixed_input_information; descriptive source table only, no ranked fair-comparison claim; dataset size: 6600; eligible count: Not reported; input information: Vina receives ground-truth ligand-centred 30 angstrom cubic search box and exhaustiveness 16; neural co-folding methods receive shared MMSeqs2 v15 MSAs; input conditions differ.; model configuration: Boltz recycle=10, diffusion samples=5; AF3 and DiffDock default parameters; restraint variants as table condition.; plinder release: unextracted; restraint parameters: Not reported; scored count: Not reported; selection: monomer proteins; single nonpolymeric ligand with sp3-carbon chiral center; allowed elements C,N,O,F,P,S,Cl,Br,I; RDKit conformer generation; ligand Tanimoto clustering 0.95; training overlap: All-entry summary includes structures before 2021-09-30; do not label held-out generalization.
- comparison
- protocol id: acquired-protocol-127e215c861a6b462f4d; dataset version: ACS Omega 2025 version of record; PMC12658688 XML retrieved 2026-09-19; split: all entries (includes Before and After training cutoff subsets); population: Plinder-L95; inputs: co-folding; adaptation: unreported; aggregation: metric-specific; inspect each result
- missing metadata
- checkpoint revision: unreported; scored count: unreported
Related records
- model: AF3
- benchmark: Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding
- dataset: Plinder-L95
- evaluation: AF3 · angle_rmsd · Plinder-L95
- evaluation: AF3 · ligand_rmsd · Plinder-L95
- evaluation: AF3 · chirality · Plinder-L95
- evaluation: AF3 · protein_rmsd · Plinder-L95
- evaluation: AF3 · bond_rmsd · Plinder-L95