Dataset Summary

This is a protein structure and protein prediction dataset for the papers GearNet (https://arxiv.org/abs/2203.06125), ESM-GearNet (https://arxiv.org/abs/2303.06275), ESM-S (https://arxiv.org/abs/2402.05856) and ProtIR (). The dataset is first processed by DeepFRI (https://www.nature.com/articles/s41467-021-23303-9) and then collected by CDConv (https://openreview.net/forum?id=P5Z-Zl9XJ7). The original files can also be downloaded from the github of CDConv (https://github.com/hehefan/Continuous-Discrete-Convolution). We upload the dataset here for the ease of downloading.

The details are shown in the following table.

Dataset	#Train	#Valid	#Test 95%	#Test 50%	#Test 30%
EnzymeCommission	15,550	1,729	1,919	1,117	720
GeneOntology	29,898	3,322	3,416	2,199	1,717
Fold	12,312	736	1,272 (Family)	1,254 (Superfamily)	718 (Fold)

Evaluation Pipeline

Please refer to ESM-S (https://github.com/DeepGraphLearning/esm-s) for the training and evaluation code.