Method

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

14 evaluations · 14 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Method: 3DCNN	Task: ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error Dataset subset: ATOM3D LBA (ATOM3D split)	1.42 rmse error · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 3DCNN on ATOM3D LBA-RMSE: Ligand binding affinity, root mean squared error Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LBA RMSE), column(3DCNN)
Method: 3DCNN	Task: ATOM3D LBA-RP: Ligand binding affinity, global Pearson correlation Dataset subset: ATOM3D LBA (ATOM3D split)	0.55 pearson_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 3DCNN on ATOM3D LBA-RP: Ligand binding affinity, global Pearson correlation Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(glob. RP), column(3DCNN)
Method: 3DCNN	Task: ATOM3D LBA-RS: Ligand binding affinity, global Spearman correlation Dataset subset: ATOM3D LBA (ATOM3D split)	0.553 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 3DCNN on ATOM3D LBA-RS: Ligand binding affinity, global Spearman correlation Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(glob. RS), column(3DCNN)
Method: 3DCNN	Task: ATOM3D LEP-AUROC: Ligand efficacy prediction Dataset subset: ATOM3D LEP (ATOM3D split)	0.589 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 3DCNN on ATOM3D LEP-AUROC: Ligand efficacy prediction Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 5, row(LEP AUROC), column(3DCNN)
Method: 3DCNN	Task: ATOM3D MSP: Mutation stability prediction Dataset subset: ATOM3D MSP (ATOM3D split)	0.574 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 3DCNN 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. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 4, row(MSP AUROC), column(3DCNN)
Method: 3DCNN	Task: ATOM3D PIP: Protein interface prediction Dataset subset: ATOM3D PIP (ATOM3D split)	0.844 auroc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 3DCNN 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. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 4, row(PIP AUROC), column(3DCNN)
Method: 3DCNN	Task: ATOM3D PSR-GLOBAL-RS: Protein structure ranking, global Spearman Dataset subset: ATOM3D PSR (ATOM3D split)	0.789 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 3DCNN on ATOM3D PSR-GLOBAL-RS: Protein structure ranking, global Spearman Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 6, row(glob. RS), column(3DCNN)
Method: 3DCNN	Task: ATOM3D PSR-MEAN-RS: Protein structure ranking, mean Spearman within a target Dataset subset: ATOM3D PSR (ATOM3D split)	0.431 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 3DCNN on ATOM3D PSR-MEAN-RS: Protein structure ranking, mean Spearman within a target Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 6, row(PSR mean RS), column(3DCNN)
Method: 3DCNN	Task: ATOM3D RES: Residue identity Dataset subset: ATOM3D RES (ATOM3D split)	0.451 accuracy fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 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. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 4, row(RES accuracy), column(3DCNN)
Method: 3DCNN	Task: ATOM3D RSR-GLOBAL-RS: RNA structure ranking, global Spearman Dataset subset: ATOM3D RSR (ATOM3D split)	0.372 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 3DCNN on ATOM3D RSR-GLOBAL-RS: RNA structure ranking, global Spearman Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 6, row(glob. RS), column(3DCNN)
Method: 3DCNN	Task: ATOM3D RSR-MEAN-RS: RNA structure ranking, mean Spearman within a target Dataset subset: ATOM3D RSR (ATOM3D split)	0.264 spearman_r correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 3DCNN on ATOM3D RSR-MEAN-RS: RNA structure ranking, mean Spearman within a target Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 6, row(RSR mean RS), column(3DCNN)
Method: 3DCNN	Task: ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap Dataset subset: ATOM3D SMP (ATOM3D split)	0.58 mae error · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 3DCNN on ATOM3D SMP-EGAP: Small molecule properties, HOMO-LUMO gap Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(SMP εgap [eV]), column(3DCNN)
Method: 3DCNN	Task: ATOM3D SMP-MU: Small molecule properties, dipole moment Dataset subset: ATOM3D SMP (ATOM3D split)	0.754 mae error · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 3DCNN on ATOM3D SMP-MU: Small molecule properties, dipole moment Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(µ [D]), column(3DCNN)
Method: 3DCNN	Task: ATOM3D SMP-U0AT: Small molecule properties, atomization energy Dataset subset: ATOM3D SMP (ATOM3D split)	3.86 mae error · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source 3DCNN on ATOM3D SMP-U0AT: Small molecule properties, atomization energy Trained and scored under the ATOM3D split for this task. Asterisks in the paper mark a run whose training data differed. Aggregation: Not reported ATOM3D: Tasks On Molecules in Three Dimensions · Table 3, row(U0at [eV]), column(3DCNN)

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