result · source checked
1.342 Median ligand RMSD
DiffDock · Median ligand RMSD · PLINDER-L95
- Tested model
- DiffDock
- Task or benchmark
- Protein–ligand pose prediction
- Dataset
- PLINDER-L95
- Procedure
- All entries; rigid-protein docking comparator; authors note this dataset contains structures seen during model training.
- Evaluation
- DiffDock: Protein–ligand pose prediction
- Evidence
- Independent external evaluation · source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1, DiffDock row, Ligand RMSD (Å) 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.
Evaluation results
Release 2026-09-16-d74d282221a9 · 1 evaluation · 1 metric row. Different protocols are not a single leaderboard.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| DiffDock: Protein–ligand pose prediction All entries; rigid-protein docking comparator; authors note this dataset contains structures seen during model training. Independent external evaluation · Evaluation metadata: needs review | ||
| 1.342 Median ligand RMSD Unit: Å · Direction: unknown | Uncertainty: not reported in legacy extract Scored: Not reported · Eligible: Not reported | source checkedImproving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Table 1, DiffDock row, Ligand RMSD (Å) column Source checking is not independent reproduction. |
Sources and history
Release 2026-09-16-d74d282221a9 · Record review: source checked
- Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction · Original source · version of record
Technical metadata and extraction receipts
Stable ID: lit-046
- areas
- molecular-interactions
- tasks
- Protein–ligand pose prediction
- printed value
- 1.342
- numeric value
- 1.342
- metric
- Median ligand RMSD
- metric direction
- unknown
- unit
- Å
- uncertainty
- Not reported
- source locator
- Table 1, DiffDock row, Ligand RMSD (Å) column
- review
- method: independent_ai_table_review; reviewer: Codex omics research agent; independent source-table review, not human review; reviewed at: 2026-09-16T10:41:16.556572+00:00; notes: JATS label is bare 1. Selected Ligand RMSD column in Plinder-L95, not Protein RMSD; retained method row without refinement settings. This verifies the central score at its source location, not every metadata field or an experimental reproduction.; evidence: {"table_xml_id": "tbl1", "row_cells": ["DiffDock", "", "", "1.342", "100", "0", "0"], "selected_cell_zero_based": 3, "selected_cell_xml": "<td align=\"center\" colspan=\"1\" rowspan=\"1\">1.342</td>", "caption": "Evaluation Metrics for Protein and Ligand Structure Prediction Performance across All Entries in the Plinder-L95 Data Set"}; artifact sha256: 78a77b9a0ab8bfa371f5b9baef3f443f4590d6e71cf864d67e90e9ebdfa7fc1b; retrieval url: https://www.ebi.ac.uk/europepmc/webservices/rest/PMC12658688/fullTextXML
- legacy id
- lit-046
- legacy row
- id: lit-046; paper id: boltz-stereochemistry-2025; domain id: molecular-interactions; task: Protein–ligand pose prediction; model: DiffDock; model version: Not reported; dataset: PLINDER-L95; dataset version: Not reported; split: Not reported; metric: Median ligand RMSD; value: 1.342; unit: Å; uncertainty: Not reported; protocol: All entries; rigid-protein docking comparator; authors note this dataset contains structures seen during model training.; source locator: Table 1, DiffDock row, Ligand RMSD (Å) column; source url: https://pmc.ncbi.nlm.nih.gov/articles/PMC12658688/; evaluation origin: independent_paper; reviewed utc: 2026-09-15T23:25:00Z
- missing metadata
- model version: not_reported_in_legacy_extract; dataset version: not_reported_in_legacy_extract; split: not_reported_in_legacy_extract; uncertainty: not_reported_in_legacy_extract
Related records
- evaluation: DiffDock: Protein–ligand pose prediction
- subject: Reported Median ligand RMSD for DiffDock