3DCNN
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 |
|---|---|---|
| 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. |
| 3DCNN on ATOM3D LBA-RP: Ligand binding affinity, global Pearson correlation Method: 3DCNNTask: 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 | ||
| 0.550 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(3DCNN) Source checking is not independent reproduction. |
| 3DCNN on ATOM3D LBA-RS: Ligand binding affinity, global Spearman correlation Method: 3DCNNTask: 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 | ||
| 0.553 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(3DCNN) Source checking is not independent reproduction. |
| 3DCNN on ATOM3D LEP-AUROC: Ligand efficacy prediction Method: 3DCNNTask: 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 | ||
| 0.589 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(3DCNN) Source checking is not independent reproduction. |
| 3DCNN on ATOM3D MSP: Mutation stability prediction Method: 3DCNNTask: ATOM3D MSP: Mutation stability predictionDataset subset: ATOM3D MSP (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 | ||
| 0.574 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(3DCNN) Source checking is not independent reproduction. |
| 3DCNN on ATOM3D PIP: Protein interface prediction Method: 3DCNNTask: ATOM3D PIP: Protein interface predictionDataset subset: ATOM3D PIP (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 | ||
| 0.844 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(3DCNN) Source checking is not independent reproduction. |
| 3DCNN on ATOM3D PSR-GLOBAL-RS: Protein structure ranking, global Spearman Method: 3DCNNTask: 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 | ||
| 0.789 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(3DCNN) Source checking is not independent reproduction. |
| 3DCNN on ATOM3D PSR-MEAN-RS: Protein structure ranking, mean Spearman within a target Method: 3DCNNTask: 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 | ||
| 0.431 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(3DCNN) Source checking is not independent reproduction. |
| 3DCNN 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 | ||
| 0.451 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(3DCNN) Source checking is not independent reproduction. |
| 3DCNN on ATOM3D RSR-GLOBAL-RS: RNA structure ranking, global Spearman Method: 3DCNNTask: 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 | ||
| 0.372 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(3DCNN) Source checking is not independent reproduction. |
| 3DCNN on ATOM3D RSR-MEAN-RS: RNA structure ranking, mean Spearman within a target Method: 3DCNNTask: 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 | ||
| 0.264 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(3DCNN) Source checking is not independent reproduction. |
| 3DCNN on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap Method: 3DCNNTask: 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 | ||
| 0.580 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(3DCNN) Source checking is not independent reproduction. |
| 3DCNN on ATOM3D SMP-MU: Small molecule properties, dipole moment Method: 3DCNNTask: 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 | ||
| 0.754 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(3DCNN) Source checking is not independent reproduction. |
| 3DCNN on ATOM3D SMP-U0AT: Small molecule properties, atomization energy Method: 3DCNNTask: 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 | ||
| 3.862 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(3DCNN) 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-3dcnn
- areas
- molecular-interactions
- source locator
- Table 3, column(3DCNN)
- missing metadata
- checkpoint revision: unreported; parameters: unextracted
Related records
- model: 3DCNN on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error
- model: 3DCNN on ATOM3D LBA-RP: Ligand binding affinity, global Pearson correlation
- model: 3DCNN on ATOM3D LBA-RS: Ligand binding affinity, global Spearman correlation
- model: 3DCNN on ATOM3D LEP-AUROC: Ligand efficacy prediction
- model: 3DCNN on ATOM3D MSP: Mutation stability prediction
- model: 3DCNN on ATOM3D PIP: Protein interface prediction
- model: 3DCNN on ATOM3D PSR-GLOBAL-RS: Protein structure ranking, global Spearman
- model: 3DCNN on ATOM3D PSR-MEAN-RS: Protein structure ranking, mean Spearman within a target
- model: 3DCNN on ATOM3D RES: Residue identity
- model: 3DCNN on ATOM3D RSR-GLOBAL-RS: RNA structure ranking, global Spearman
- model: 3DCNN on ATOM3D RSR-MEAN-RS: RNA structure ranking, mean Spearman within a target
- model: 3DCNN on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap
- model: 3DCNN on ATOM3D SMP-MU: Small molecule properties, dipole moment
- model: 3DCNN on ATOM3D SMP-U0AT: Small molecule properties, atomization energy