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Adds Dataset Card for the ProstT5Dataset
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@mheinz
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when you find the time, please review the content of this card and check which licence is suitable.
README.md
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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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---
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# Dataset Card for "ProstT5Dataset"
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-
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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: cc
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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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# ⚠ Currently under review ⚠
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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:** TBD
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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 | | |
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