Table 1 A catalog of protein feature datasets that can be used in ML
Database/dataset | Wikidata entry | Domain Level | Residue level | Atom Level | Residue–residue graph | \(\varvec{2^{\circ }}\) Structure | Electrostatics and charge | Surface and curvature | Protein interaction sites | Train/validation splits | Clusters | Evolutionary info | File format |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PDB [9] | Â | \(\checkmark\) | \(\checkmark ^{\dagger }\) | Â | \(\checkmark\) | Â | \(\checkmark\) | Â | Â | \(\checkmark\) | Â | Web, mmCIF, MMTF | |
UniProt [13] | Â | \(\checkmark\) | Â | Â | \(\checkmark\) | Â | Â | Â | Â | \(\checkmark\) | Â | Web, ReST | |
CATH [14] | \(\checkmark\) | \(\checkmark\) | \(\checkmark ^{\dagger }\) | Â | Â | Â | Â | Â | Â | \(\checkmark\) | \(\checkmark\) | PDB, ReST | |
FEATURE [15] | Â | \(\checkmark\) | \(\checkmark\) | Â | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | Â | Â | Â | Â | ASCII | |
PredictProtein [16] | Â | \(\checkmark\) | Â | Â | \(\checkmark\) | Â | \(\checkmark\) | \(\checkmark\) | Â | Â | \(\checkmark\) | Web, ReST, JSON | |
DescribePROT [17] | Â | \(\checkmark\) | Â | Â | Â | Â | \(\checkmark\) | \(\checkmark\) | Â | Â | \(\checkmark\) | Web, JSON | |
ATOM3D/DIPS [18] | Â | \(\checkmark\) | \(\checkmark ^{\dagger }\) | Â | Â | Â | Â | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | Â | JSON, PyTorch | |
ProteinNet [19] | Â | \(\checkmark\) | \(\checkmark ^{\dagger }\) | Â | \(\checkmark\) | Â | Â | Â | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | TensorFlow | |
SidechainNet [20] | Â | \(\checkmark\) | \(\checkmark ^{\dagger }\) | Â | \(\checkmark\) | Â | Â | Â | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | PyTorch, Pickle | |
Prop3D [this work] | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | Â | \(\checkmark\) | \(\checkmark\) | \(\checkmark\) | HDF, HSDS, PyTorch |