GNN
Network implemented and trained by the ATOM3D authors over the three-dimensional structure.
Overview
Network implemented and trained by the ATOM3D authors over the three-dimensional structure.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
Release 2026-09-17-134cd1815de8 · 14 evaluations · 14 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 |
|---|---|---|
| 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. |
| GNN on ATOM3D LBA-RP: Ligand binding affinity, global Pearson correlation Method: GNNTask: ATOM3D LBA-RP: Ligand binding affinity, global Pearson correlationDataset 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 | ||
| 0.545 pearson_r Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(glob. RP), column(GNN) Source checking is not independent reproduction. |
| GNN on ATOM3D LBA-RS: Ligand binding affinity, global Spearman correlation Method: GNNTask: ATOM3D LBA-RS: Ligand binding affinity, global Spearman correlationDataset 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 | ||
| 0.533 spearman_r Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(glob. RS), column(GNN) Source checking is not independent reproduction. |
| GNN on ATOM3D LEP-AUROC: Ligand efficacy prediction Method: GNNTask: ATOM3D LEP-AUROC: Ligand efficacy predictionDataset subset: ATOM3D LEP (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 | ||
| 0.681 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LEP AUROC), column(GNN) Source checking is not independent reproduction. |
| GNN on ATOM3D MSP: Mutation stability prediction 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 | ||
| 0.609 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 4, row(MSP AUROC), column(GNN) Source checking is not independent reproduction. |
| GNN on ATOM3D PIP: Protein interface prediction 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 | ||
| 0.669 auroc Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 4, row(PIP AUROC), column(GNN) Source checking is not independent reproduction. |
| GNN on ATOM3D PSR-GLOBAL-RS: Protein structure ranking, global Spearman Method: GNNTask: ATOM3D PSR-GLOBAL-RS: Protein structure ranking, global SpearmanDataset subset: ATOM3D PSR (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 | ||
| 0.750 spearman_r Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 6, row(glob. RS), column(GNN) Source checking is not independent reproduction. |
| GNN on ATOM3D PSR-MEAN-RS: Protein structure ranking, mean Spearman within a target Method: GNNTask: ATOM3D PSR-MEAN-RS: Protein structure ranking, mean Spearman within a targetDataset subset: ATOM3D PSR (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 | ||
| 0.411 spearman_r Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 6, row(PSR mean RS), column(GNN) Source checking is not independent reproduction. |
| GNN on ATOM3D RES: Residue identity 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 | ||
| 0.082 accuracy Unit: fraction · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 4, row(RES accuracy), column(GNN) Source checking is not independent reproduction. |
| GNN on ATOM3D RSR-GLOBAL-RS: RNA structure ranking, global Spearman Method: GNNTask: ATOM3D RSR-GLOBAL-RS: RNA structure ranking, global SpearmanDataset subset: ATOM3D RSR (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 | ||
| 0.512 spearman_r Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 6, row(glob. RS), column(GNN) Source checking is not independent reproduction. |
| GNN on ATOM3D RSR-MEAN-RS: RNA structure ranking, mean Spearman within a target Method: GNNTask: ATOM3D RSR-MEAN-RS: RNA structure ranking, mean Spearman within a targetDataset subset: ATOM3D RSR (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 | ||
| 0.234 spearman_r Unit: correlation · Direction: higher | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 6, row(RSR mean RS), column(GNN) Source checking is not independent reproduction. |
| GNN on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap Method: GNNTask: ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gapDataset subset: ATOM3D SMP (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 | ||
| 0.137 mae Unit: error · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(SMP εgap [eV]), column(GNN) Source checking is not independent reproduction. |
| GNN on ATOM3D SMP-MU: Small molecule properties, dipole moment Method: GNNTask: ATOM3D SMP-MU: Small molecule properties, dipole momentDataset subset: ATOM3D SMP (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 | ||
| 0.501 mae Unit: error · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(µ [D]), column(GNN) Source checking is not independent reproduction. |
| GNN on ATOM3D SMP-U0AT: Small molecule properties, atomization energy Method: GNNTask: ATOM3D SMP-U0AT: Small molecule properties, atomization energyDataset subset: ATOM3D SMP (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 | ||
| 1.424 mae Unit: error · Direction: lower | Uncertainty: Not reported Scored: Not reported · Eligible: Not reported | source checkedATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(U0at [eV]), column(GNN) 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.
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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-method-gnn
- areas
- molecular-interactions
- source locator
- Table 3, column(GNN)
- missing metadata
- checkpoint revision: unreported; parameters: unextracted
Related records
- model: GNN on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error
- model: GNN on ATOM3D LBA-RP: Ligand binding affinity, global Pearson correlation
- model: GNN on ATOM3D LBA-RS: Ligand binding affinity, global Spearman correlation
- model: GNN on ATOM3D LEP-AUROC: Ligand efficacy prediction
- model: GNN on ATOM3D MSP: Mutation stability prediction
- model: GNN on ATOM3D PIP: Protein interface prediction
- model: GNN on ATOM3D PSR-GLOBAL-RS: Protein structure ranking, global Spearman
- model: GNN on ATOM3D PSR-MEAN-RS: Protein structure ranking, mean Spearman within a target
- model: GNN on ATOM3D RES: Residue identity
- model: GNN on ATOM3D RSR-GLOBAL-RS: RNA structure ranking, global Spearman
- model: GNN on ATOM3D RSR-MEAN-RS: RNA structure ranking, mean Spearman within a target
- model: GNN on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap
- model: GNN on ATOM3D SMP-MU: Small molecule properties, dipole moment
- model: GNN on ATOM3D SMP-U0AT: Small molecule properties, atomization energy