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--- |
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dataset_info: |
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features: |
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- name: input_id_x |
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sequence: int64 |
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- name: input_id_y |
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sequence: int64 |
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splits: |
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- name: test |
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num_bytes: 1087504 |
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num_examples: 474 |
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- name: valid |
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num_bytes: 1124160 |
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num_examples: 474 |
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- name: train |
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num_bytes: 65391887792 |
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num_examples: 17070828 |
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download_size: 810671738 |
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dataset_size: 65394099456 |
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license: mit |
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task_categories: |
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- text-generation |
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tags: |
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- biology |
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size_categories: |
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- 10M<n<100M |
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--- |
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# Dataset Card for "ProstT5Dataset" |
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* **Contributors:** Michael Heinzinger and Konstantin Weissenow, Joaquin Gomez Sanchez and Adrian Henkel, Martin Steinegger and Burkhard Rost |
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* **Licence:** MIT |
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## Table of Contents |
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- [Overview](#overview) |
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- [Dataset Description](#dataset-description) |
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- [Data Collection and Annotation](#data-collection-and-annotation) |
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- [Data Splits](#data-splits) |
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- [Dataset Structure](#dataset-structure) |
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- [Data Fields](#data-fields) |
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- [Data Instances](#data-instances) |
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- [Data Considerations](#data-considerations) |
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- [Social Impact of Dataset](#social-impact-of-dataset) |
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- [Discussion of Biases](#discussion-of-biases) |
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- [Other Known Limitations](#other-known-limitations) |
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- [Licensing Information](#licensing-information) |
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- [Citation Information](#citation-information) |
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- [Contributions](#contributions) |
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## Overview |
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The ProstT5Dataset is a curated collection of *tokenized* protein sequences and their corresponding structure sequences (3Di). |
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It is derived from the [AlphaFold Protein Structure Database](https://alphafold.ebi.ac.uk/) and includes various steps of clustering and quality filtering. |
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To capture 3D information of the sequence, the [3Di structure string representation](https://www.nature.com/articles/s41587-023-01773-0#Sec2) is leveraged. This format |
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captures the spatial relationship of each residue to its neighbors in 3D space, effectively translating the 3D information of the sequence. |
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The sequence tokens are generated using the [ProstT5 Tokenizer](https://huggingface.co/Rostlab/ProstT5). |
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## Data Fields |
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- **input_id_x** (3Di Tokens): Corresponding tokenized 3Di structure representation sequences derived from the proteins. |
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- **input_id_y** (Amino Acid Tokens): Tokenized amino acid sequences of proteins. |
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## Dataset Description |
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We compare basic protein properties (sequence length, amino acid composition, 3Di-distribution) between our |
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dataset (training, validation, test sets) and proteins obtained from the [Protein Data Bank (PDB)](https://www.rcsb.org/). Key findings include similar amino acid distributions across datasets, |
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an overrepresentation of certain 3Di-tokens (d, v, p) and helical structures in AlphaFold2 predictions compared to PDB, and a tendency for shorter protein |
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lengths in this dataset (average 206-238) relative to PDB proteins (average 255). The analysis also highlights the relationship between |
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3Di states and secondary structures, with a notable distinction in strand-related tokens between datasets. |
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## Data Collection and Annotation |
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The dataset began with the AlphaFold Protein Structure Database , undergoing a two-step clustering process and one step of quality filtering: |
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1. *First Clustering:* 214M UniprotKB protein sequences were clustered using MMseqs2, resulting in 52M clusters based on pairwise sequence identity. |
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2. *Second Clustering:* Foldseek further clustered these proteins into 18.8M clusters, expanded to 18.6M proteins by adding diverse members. |
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3. *Quality Filtering:* Removed proteins with low pLDDT scores, short lengths, and highly repetitive 3Di-strings. The final training split contains 17M proteins. |
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## Citation |
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``` |
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@article{heinzinger2023prostt5, |
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title={ProstT5: Bilingual language model for protein sequence and structure}, |
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author={Heinzinger, Michael and Weissenow, Konstantin and Sanchez, Joaquin Gomez and Henkel, Adrian and Steinegger, Martin and Rost, Burkhard}, |
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journal={bioRxiv}, |
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pages={2023--07}, |
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year={2023}, |
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publisher={Cold Spring Harbor Laboratory} |
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} |
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``` |
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## Tokens to Character Mapping |
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| Amino Acid Representation | 3DI | Special Tokens | |
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|---------------------------|-----------|--------------------| |
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| 3: A | 128: a | 0: \<pad\> | |
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| 4: L | 129: l | 1: \</s\> | |
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| 5: G | 130: g | 2: \<unk\> | |
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| 6: V | 131: v | 148: \<fold2AA\> | |
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| 7: S | 132: s | 149: \<AA2fold\> | |
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| 8: R | 133: r | | |
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| 9: E | 134: e | | |
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| 10: D | 135: d | | |
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| 11: T | 136: t | | |
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| 12: I | 137: i | | |
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| 13: P | 138: p | | |
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| 14: K | 139: k | | |
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| 15: F | 140: f | | |
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| 16: Q | 141: q | | |
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| 17: N | 142: n | | |
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| 18: Y | 143: y | | |
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| 19: M | 144: m | | |
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| 20: H | 145: h | | |
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| 21: W | 146: w | | |
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| 22: C | 147: c | | |
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| 23: X | | | |
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| 24: B | | | |
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| 25: O | | | |
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| 26: U | | | |
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| 27: Z | | | |
