ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error
Ligand binding affinity, root mean squared error. Scored with RMSE on ATOM3D LBA. Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed.
Overview
Ligand binding affinity, root mean squared error. Scored with RMSE on ATOM3D LBA. Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed.
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.
- 3DCNN on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error
- ENN on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error
- GNN on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error
- [Karimi et al., 2019] on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error
- [Öztürk et al., 2018] on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error
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.
Published comparisons
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies. The pooled view gathers every source table that reports the same metric and names what it does not hold constant.
ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error
rmse (error) · Lower values are better for this metric.
Every method ATOM3D reports on Ligand binding affinity, root mean squared error, scored with RMSE on ATOM3D LBA.
- 3DCNN · Method · Author-reported evaluation1.416
- GNN · Method · Author-reported evaluation1.601
- ENN · Method · Author-reported evaluation1.568
- [Öztürk et al., 2018] · Configuration · Author-reported evaluation1.565
- [Karimi et al., 2019] · Configuration · Author-reported evaluation1.893
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.
ATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LBA RMSE)Values, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| 3DCNN · Method | 1.416 error | Not reported | Author-reported evaluation · source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LBA RMSE), column(3DCNN) |
| GNN · Method | 1.601 error | Not reported | Author-reported evaluation · source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LBA RMSE), column(GNN) |
| ENN · Method | 1.568 error | Not reported | Author-reported evaluation · source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LBA RMSE), column(ENN) |
| [Öztürk et al., 2018] · Configuration | 1.565 error | Not reported | Author-reported evaluation · source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LBA RMSE), column([Öztürk et al., 2018]) |
| [Karimi et al., 2019] · Configuration | 1.893 error | Not reported | Author-reported evaluation · source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LBA RMSE), column([Karimi et al., 2019]) |
Scope and limitations
- Author-reported numbers, source checked but not independently reproduced.
- MAE and RMSE are errors, better when lower. The other metrics are better when higher.
- Comparison methods are named by the citation the table prints; the paper's text says which method each is.
- The paper marks some runs with an asterisk to say their training data differed, though the splitting criteria were the same.
Source transcription and grouping reviewed by automated source review on 2026-09-18. These experiments were not independently reproduced by rewire.
Tested entities and results
Release 2026-09-17-134cd1815de8 · 5 evaluations · 5 metric rows. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| 3DCNN on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error Method: 3DCNNTask: ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared errorDataset subset: ATOM3D LBA (ATOM3D split) Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Author-reported evaluation · Evaluation metadata: source checked | ||
| 1.416 rmse Unit: error · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LBA RMSE), column(3DCNN) Source checking is not independent reproduction. |
| ENN on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error Method: ENNTask: ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared errorDataset subset: ATOM3D LBA (ATOM3D split) Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Author-reported evaluation · Evaluation metadata: source checked | ||
| 1.568 rmse Unit: error · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LBA RMSE), column(ENN) Source checking is not independent reproduction. |
| GNN on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error Method: GNNTask: ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared errorDataset subset: ATOM3D LBA (ATOM3D split) Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Author-reported evaluation · Evaluation metadata: source checked | ||
| 1.601 rmse Unit: error · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LBA RMSE), column(GNN) Source checking is not independent reproduction. |
| [Karimi et al., 2019] on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error Configuration: [Karimi et al., 2019]Task: ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared errorDataset subset: ATOM3D LBA (ATOM3D split) Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Author-reported evaluation · Evaluation metadata: source checked | ||
| 1.893 rmse Unit: error · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LBA RMSE), column([Karimi et al., 2019]) Source checking is not independent reproduction. |
| [Öztürk et al., 2018] on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error Configuration: [Öztürk et al., 2018]Task: ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared errorDataset subset: ATOM3D LBA (ATOM3D split) Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Author-reported evaluation · Evaluation metadata: source checked | ||
| 1.565 rmse Unit: error · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LBA RMSE), column([Öztürk et al., 2018]) Source checking is not independent reproduction. |
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
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of discovery-benchmark-atom3d Individual claims | ATOM3D: Tasks On Molecules in Three Dimensions Table 5, row(LBA RMSE) Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | source checked automated source review · 2026-09-18 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: atom3d-association-lba-rmse Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
Release 2026-09-17-134cd1815de8 · Record review: source checked
1 source records and release history
- ATOM3D: Tasks On Molecules in Three Dimensions · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Technical metadata and extraction receipts
Stable ID: atom3d-task-lba-rmse
- areas
- molecular-interactions
- tasks
- Ligand binding affinity, root mean squared error
- metric
- RMSE
- metric direction
- lower
- dataset
- ATOM3D LBA
- protocol
- Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed.
- source locator
- Table 5, row(LBA RMSE)
- comparison panels
- id: atom3d-panel-lba-rmse; title: ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error; protocol id: atom3d-task-lba-rmse; dataset id: atom3d-dataset-atom3d-lba; metric: rmse; unit: error; direction: lower; result ids: atom3d-result-3dcnn-lba-rmse-rmse; atom3d-result-gnn-lba-rmse-rmse; atom3d-result-enn-lba-rmse-rmse; atom3d-result-zt-rk-et-al-2018-lba-rmse-rmse; atom3d-result-karimi-et-al-2019-lba-rmse-rmse; source ids: evidence-expansion-atom3d-92656c20; source locator: Table 5, row(LBA RMSE); context: Every method ATOM3D reports on Ligand binding affinity, root mean squared error, scored with RMSE on ATOM3D LBA.; caveats: Author-reported numbers, source checked but not independently reproduced.; MAE and RMSE are errors, better when lower. The other metrics are better when higher.; Comparison methods are named by the citation the table prints; the paper's text says which method each is.; The paper marks some runs with an asterisk to say their training data differed, though the splitting criteria were the same.; review: method: automated_source_review; date: 2026-09-18
Related records
- part of: ATOM3D
- subject: ATOM3D LBA-RMSE: part of discovery-benchmark-atom3d
- benchmark: 3DCNN on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error
- benchmark: ENN on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error
- benchmark: GNN on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error
- benchmark: [Karimi et al., 2019] on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error
- benchmark: [Öztürk et al., 2018] on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error