Datasets
PLINDER and PDBbind2020 complexes; PLINDER subsets use ligand-similarity filtering.
Task
Protein–ligand pose prediction
Protein–ligand pose assessment distinguishes geometric accuracy from stereochemical validity and examines temporal distribution shift.
Sources
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44Overview
Metrics
Protein and ligand RMSD, chirality reproduction, bond-length RMSD and bond-angle RMSD; aggregate definitions vary by metric.
Allowed inputs
Complex prediction inputs; restraint-conditioned variants are explicitly separate comparisons.
Sources
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44Evaluation procedure diagram
How it worksComputational evaluation flow
Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol.
Sources
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44limited source coverage · Automated source review, 2026-09-16. All specifications and missing details
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
2 evaluations · 2 results. Different protocols are not a single leaderboard.
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: Boltz-1 | Task: Protein–ligand pose prediction Dataset: PLINDER-L95 | 1.39 Median ligand RMSD Å · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceBoltz-1: Protein–ligand pose prediction All entries; authors note this dataset contains structures seen during model training. Aggregation: Not reported Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1, Boltz-1 row, Ligand RMSD (Å) column |
| Configuration: DiffDock | Task: Protein–ligand pose prediction Dataset: PLINDER-L95 | 1.34 Median ligand RMSD Å · unknown Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceDiffDock: Protein–ligand pose prediction All entries; rigid-protein docking comparator; authors note this dataset contains structures seen during model training. Aggregation: Not reported Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1, DiffDock row, Ligand RMSD (Å) column |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
Methods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation methodology
PLINDER and PDBbind2020 complexes; PLINDER subsets use ligand-similarity filtering. Before/After subsets are separated by the structure-prediction training cutoff; stricter subsets additionally filter protein and ligand similarity. Protein and ligand RMSD, chirality reproduction, bond-length RMSD and bond-angle RMSD; aggregate definitions vary by metric. AlphaFold3, Boltz-1 and restraint variants; AutoDock Vina and DiffDock for applicable ligand metrics. Temporal and similarity-based subsets are examined separately; Before-set scores include structures potentially seen in training. The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim.
Sources
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44Recorded evaluations
Each evaluation records what was tested and under which conditions.
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Strengths, limitations and unresolved questions
Strengths and limitations
Strengths and considerations
- Pose agreement and stereochemical validity are assessed as different criteria.
Sources
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44
Limitations and conditions
- Rigid-receptor docking comparators cannot meaningfully supply every protein-structure metric.
Sources
Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44
Profile review details
Relevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged.
Stable record: reported-task-bf513ed6db92c5Specifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-16. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | PLINDER and PDBbind2020 complexes; PLINDER subsets use ligand-similarity filtering.SourcesImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 |
| Splits | Before/After subsets are separated by the structure-prediction training cutoff; stricter subsets additionally filter protein and ligand similarity.SourcesImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 |
| Metrics | Protein and ligand RMSD, chirality reproduction, bond-length RMSD and bond-angle RMSD; aggregate definitions vary by metric.SourcesImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 |
| Baselines | AlphaFold3, Boltz-1 and restraint variants; AutoDock Vina and DiffDock for applicable ligand metrics.SourcesImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 |
| Leakage controls | Temporal and similarity-based subsets are examined separately; Before-set scores include structures potentially seen in training.SourcesImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 |
| Uncertainty | The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. · Not reported in inspected sourcesSourcesImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 |
| Entity type | Paper-specific computational evaluation protocol.SourcesImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 |
| Organisms | PLINDER and PDBbind subsets are filtered by structure, time and similarity for the broad benchmark. Their curation section does not tabulate species coverage. The separately described human MDM2 case is not the organism scope of the full benchmark. · Not reported in inspected sourcesSourcesImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Dataset selection; separate MDM2 case-study setup |
| Assays | Protein–ligand structures with stereochemical and pose references.SourcesImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 |
| Allowed inputs | Complex prediction inputs; restraint-conditioned variants are explicitly separate comparisons.SourcesImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 |
| Adaptation | Pretrained structure predictors evaluated across cutoff-defined subsets and restraint variants.SourcesImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Papers and result coverage
Last literature check: 2026-09-17. Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
| Paper or primary resource | Version | Reference |
|---|---|---|
| Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction | version of record | Read source |
Historical gaps recorded on 2026-09-17
The catalogue now holds 2 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
- complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.
- exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.
Search and extraction details
primary comparison tables located
Searches
- Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction 10.1021/acsomega.5c07675
Evidence locations
- 1; XML table tbl1
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.
18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Diagram caption Conceptual summary of the cited evaluation; exact task configuration and source version remain part of the protocol. Individual claims | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Diagram steps
| Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Diagram title Computational evaluation flow Individual claims | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Datasets PLINDER and PDBbind2020 complexes; PLINDER subsets use ligand-similarity filtering. Individual claims | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Splits Before/After subsets are separated by the structure-prediction training cutoff; stricter subsets additionally filter protein and ligand similarity. Individual claims | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Adaptation Pretrained structure predictors evaluated across cutoff-defined subsets and restraint variants. Individual claims | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Metrics Protein and ligand RMSD, chirality reproduction, bond-length RMSD and bond-angle RMSD; aggregate definitions vary by metric. Individual claims | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Baselines AlphaFold3, Boltz-1 and restraint variants; AutoDock Vina and DiffDock for applicable ligand metrics. Individual claims | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Leakage controls Temporal and similarity-based subsets are examined separately; Before-set scores include structures potentially seen in training. Individual claims | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 Version: version of record | source checked automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Uncertainty The cited text-accessible evaluation sections give no confidence-interval, resampling or repeat-run error-bar specification. Image-only tables and uninspected supplements are outside this absence claim. Individual claims | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44 Version: version of record | unreported automated source review · 2026-09-16 Audit detailsRelevant full-paper computational evaluation sections, tables/captions and cited supplementary task passages were reviewed. Reporting omissions are scoped to the inspected sources. Original numerical results are unchanged. Field: 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 2026-09-29-06401fd5b220 · Record review: needs review
2 source records and release history
- Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Original source · version of record
- Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Original source · version of record
Technical metadata and extraction receipts
Stable ID: reported-task-bf513ed6db92c5
- areas
- molecular-interactions
- tasks
- Protein–ligand pose prediction
- entity level
- task
- version
- Not reported
- task
- Protein–ligand pose prediction
- scope note
- Paper-specific evaluation task; protocol completeness requires further extraction.
- benchmark research
- review date: 2026-09-17; status: primary_comparison_tables_located; primary sources: evidence-expansion-boltz-stereochemistry-2025-78a77b9a; inspected locators: 1; XML table tbl1; searched queries: Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction 10.1021/acsomega.5c07675; gaps: complete numerical transcription and independent cell review: Full primary artifact and table inventory preserved; no new numeric row is published from this audit alone.; exact checkpoint hashes and per-method scored denominators: Table labels alone do not establish these fields; do not infer checkpoint or scored count from model name or dataset size.; claim scope: Dated primary-source discovery and protocol/table screening. Source checking does not mean experimental reproduction. Only separately extracted and independently reviewed numeric batches are publishable.
- historical missing metadata
- protocol version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract
- metadata review scope
- historical_missing_metadata preserves the original discovery state. Current descriptive evidence and missingness are recorded in profile.facts; numerical-result review is separate.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: This source-scoped record identifies the biological prediction task and holds its paper context. Preserve the existing task identity; exact split, model adaptation and scoring remain in linked evaluations or separate protocol records.; source ids: boltz-stereochemistry-2025; source locator: Methods: Benchmark Dataset; Evaluation Metrics; Results: Table 1; cached text lines 8–14, 41–44; ambiguities: A paper- or suite-specific task may constrain some inputs or metrics; that alone does not make it interchangeable with a complete versioned protocol. No protocol equivalence is inferred.; Some legacy profile Entity type facts use the generic phrase computational evaluation protocol. That boilerplate is not sufficient to establish a single fixed protocol identity or to merge this task with another protocol record.
Related records
- dataset: PLINDER-L95
- benchmark: Boltz-1: Protein–ligand pose prediction
- benchmark: DiffDock: Protein–ligand pose prediction