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Fix dataset names in README #65

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merged 2 commits into from
Jan 3, 2024
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Fix dataset names in README #65

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7f0f26a
Fix minor virtual angle feature doc
chaitjo Dec 25, 2023
4eadea1
Fix dataset names
chaitjo Jan 3, 2024
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14 changes: 7 additions & 7 deletions README.md
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Expand Up @@ -404,11 +404,11 @@ Pre-training corpuses (with the exception of `pdb`, `cath`, and `astral`) are pr
| `go-bp` | Gene Ontology prediction (Biological Process) | [Gligorijevic et al](https://www.nature.com/articles/s41467-021-23303-9) | [CC-BY 4.0](https://www.nature.com/articles/s41467-021-23303-9)|
| `go-cc` | Gene Ontology (Cellular Component) | [Gligorijevic et al](https://www.nature.com/articles/s41467-021-23303-9) | [CC-BY 4.0](https://www.nature.com/articles/s41467-021-23303-9) |
| `go-mf` | Gene Ontology (Molecular Function) | [Gligorijevic et al](https://www.nature.com/articles/s41467-021-23303-9) | [CC-BY 4.0](https://www.nature.com/articles/s41467-021-23303-9) |
| `ec-reaction` | Enzyme Commission (EC) Number Prediction | [Hermosilla et al.](https://arxiv.org/abs/2007.06252) | [MIT](https://github.com/phermosilla/IEConv_proteins/blob/master/LICENSE)
| `fold-fold` | Fold prediction, split at the fold level | [Hou et al.](https://academic.oup.com/bioinformatics/article/34/8/1295/4708302) | [CC-BY 4.0](https://academic.oup.com/bioinformatics/article/34/8/1295/4708302)
| `fold-family` | Fold prediction, split at the family level | [Hou et al.](https://academic.oup.com/bioinformatics/article/34/8/1295/4708302) | [CC-BY 4.0](https://academic.oup.com/bioinformatics/article/34/8/1295/4708302)
| `fold-superfamily` | Fold prediction, split at the superfamily level | [Hou et al.](https://academic.oup.com/bioinformatics/article/34/8/1295/4708302) | [CC-BY 4.0](https://academic.oup.com/bioinformatics/article/34/8/1295/4708302)
| `masif-site` | Protein-protein interaction site prediction | [Gainza et al.](https://www.nature.com/articles/s41592-019-0666-6) | [Apache 2.0](https://github.com/LPDI-EPFL/masif/blob/master/LICENSE)
| `ec_reaction` | Enzyme Commission (EC) Number Prediction | [Hermosilla et al.](https://arxiv.org/abs/2007.06252) | [MIT](https://github.com/phermosilla/IEConv_proteins/blob/master/LICENSE)
| `fold_fold` | Fold prediction, split at the fold level | [Hou et al.](https://academic.oup.com/bioinformatics/article/34/8/1295/4708302) | [CC-BY 4.0](https://academic.oup.com/bioinformatics/article/34/8/1295/4708302)
| `fold_family` | Fold prediction, split at the family level | [Hou et al.](https://academic.oup.com/bioinformatics/article/34/8/1295/4708302) | [CC-BY 4.0](https://academic.oup.com/bioinformatics/article/34/8/1295/4708302)
| `fold_superfamily` | Fold prediction, split at the superfamily level | [Hou et al.](https://academic.oup.com/bioinformatics/article/34/8/1295/4708302) | [CC-BY 4.0](https://academic.oup.com/bioinformatics/article/34/8/1295/4708302)
| `masif_site` | Protein-protein interaction site prediction | [Gainza et al.](https://www.nature.com/articles/s41592-019-0666-6) | [Apache 2.0](https://github.com/LPDI-EPFL/masif/blob/master/LICENSE)
| `metal_3d` | Zinc Binding Site Prediction | [Duerr et al.](https://www.nature.com/articles/s41467-023-37870-6) | [MIT](https://zenodo.org/record/7594085)
| `ptm` | Post Translational Modification Side Prediction | [Yan et al.](https://www.sciencedirect.com/science/article/pii/S2667237523000450?via%3Dihub) | [CC-BY 4.0](https://zenodo.org/record/7655709) |

Expand Down Expand Up @@ -450,8 +450,8 @@ N.B. All angular features are provided in [sin, cos] transformed form. E.g.: $\t
| ----------- | ----------- | ----------- |
| `residue_type` | One-hot encoding of amino acid type | 21 |
| `positional_encoding` | Transformer-like positional encoding of sequence position | 16 |
| `alpha` | Virtual torsion angle defined by four $C_\alpha$ atoms of residues $I_{-1},I,I_{+1},I_{+2}$ | 2 |
| `kappa` | Virtual bond angle (bend angle) defined by the three $C_\alpha$ atoms of residues $I_{-2},I,_{+2}$ | 2 |
| `alpha` | Virtual torsion angle defined by four $C_\alpha$ atoms of residues $I_{-1}, I, I_{+1}, I_{+2}$ | 2 |
| `kappa` | Virtual bond angle (bend angle) defined by the three $C_\alpha$ atoms of residues $I_{-2}, I, I_{+2}$ | 2 |
| `dihedrals` | Backbone dihedral angles $(\phi, \psi, \omega)$ | 6 |
| `sidechain_torsions` | Sidechain torsion angles $(\chi_{1-4})$ | 8 |

Expand Down
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