Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction
2025 · version of record · Peer-reviewed
What this source contributed
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Results
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Claims
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- AF3: family AlphaFold 3: Family AlphaFold 3 (Molecular Structure Prediction; Table 1 AF3 row; Figure 2 caption)
- Boltz R: family Boltz: Family Boltz (Methods: Molecular Structure Prediction; Results: Structure Prediction Using Restraint-Guided Inference; Table 1)
- Boltz R1: family Boltz: Family Boltz (Methods: Molecular Structure Prediction; Results: Structure Prediction Using Restraint-Guided Inference; Table 1)
- Boltz Rc: family Boltz: Family Boltz (Methods: Molecular Structure Prediction; Results: Structure Prediction Using Restraint-Guided Inference; Table 1)
- Boltz-1: family Boltz: Family Boltz (Methods: Molecular Structure Prediction; Results: Structure Prediction Using Restraint-Guided Inference; Table 1)
- Boltz-1: family Boltz: Family Boltz (Methods: Molecular Structure Prediction; Results: Structure Prediction Using Restraint-Guided Inference; Table 1)
- Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries: benchmark membership: Part of PLINDER (Table 1 (XML tbl1); row DiffDock; column ligand_rmsd; footnote a)
- Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries: benchmark membership: Part of PLINDER (Table 1 (XML tbl1); row AF3; column protein_rmsd; footnote a)
- Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries: benchmark membership: Part of PLINDER (Table 1 (XML tbl1); row Vina; column ligand_rmsd; footnote a)
- Reported Median ligand RMSD for Boltz-1: Printed value 1.393 (Table 1, Boltz-1 row, Ligand RMSD (Å) column)
- Reported Median ligand RMSD for DiffDock: Printed value 1.342 (Table 1, DiffDock row, Ligand RMSD (Å) column)
Models, benchmarks and other records
Configurations (9)
Tasks (1)
Protocols (3)
- Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · co-folding
- Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · docking with ground-truth-centred search box
- Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95 · rigid-receptor docking
Datasets (1)
Dataset subsets (1)
Evaluations (9)
- AF3 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95
- Boltz R · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95
- Boltz R1 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95
- Boltz Rc · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95
- Boltz-1 · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95
- Boltz-1: Protein–ligand pose prediction
- DiffDock · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95
- DiffDock: Protein–ligand pose prediction
- Vina · Paper-specific Plinder-L95 stereochemistry assessment; Table 1 all entries · Plinder-L95
Evidence
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Evidence table
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Artifact retrieved at 2026-09-16T10:41:16.555674+00:00 Source metadata | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Artifact SHA-256 78a77b9a0ab8bfa371f5b9baef3f443f4590d6e71cf864d67e90e9ebdfa7fc1b Source metadata | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Artifact url https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12658688/fullTextXML Source metadata | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Doi 10.1021/acsomega.5c07675 Source metadata | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Missing metadata: licence: reason unextracted Source metadata | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Publication status peer_reviewed Source metadata | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Retrieved at 2026-09-15T23:25:00Z Source metadata | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Scope decision included Source metadata | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Url https://pmc.ncbi.nlm.nih.gov/articles/PMC12658688/ Source metadata | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Version version of record Source metadata | Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction No field-specific location recorded Version: version of record | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: discovered
Primary paper retained with its original identifier. Metadata inherited from the literature collection; individual result checks are separate.
Technical metadata and extraction receipts
Stable ID: boltz-stereochemistry-2025
- areas
- molecular-interactions
- url
- https://pmc.ncbi.nlm.nih.gov/articles/PMC12658688/
- version
- version of record
- retrieved at
- 2026-09-15T23:25:00Z
- doi
- 10.1021/acsomega.5c07675
- publication status
- peer_reviewed
- year
- 2025
- artifact sha256
- 78a77b9a0ab8bfa371f5b9baef3f443f4590d6e71cf864d67e90e9ebdfa7fc1b
- artifact url
- https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12658688/fullTextXML
- artifact retrieved at
- 2026-09-16T10:41:16.555674+00:00
- scope decision
- included
- missing metadata
- licence: reason: unextracted