metadata
license: apache-2.0
language:
- en
tags:
- Protein Langauge Model
- AI for Drug Discovery
- AI for Science
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.