Datasets:
Modalities:
Text
Formats:
csv
Size:
1K - 10K
Tags:
protein-protein-interaction
bioinformatics
protein-sequences
interface-prediction
partner-aware
License:
File size: 5,696 Bytes
cec659f 8aabf32 cec659f b9c4e80 cec659f b9c4e80 cec659f b9c4e80 cec659f b9c4e80 cec659f | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 | ---
license: gpl-3.0
pretty_name: SPPIDER-seq Datasets
tags:
- protein-protein-interaction
- bioinformatics
- protein-sequences
- interface-prediction
- partner-aware
configs:
- config_name: peptide-centric
data_files:
- split: train
path: pep_train_ids.tsv
- split: validation
path: pep_val_ids.tsv
- split: blind
path: pep_blind_ids.tsv
- config_name: receptor-centric
data_files:
- split: train
path: rec_train_ids.tsv
- split: validation
path: rec_val_ids.tsv
- split: blind
path: rec_blind_ids.tsv
---
# SPPIDER-seq Datasets
Datasets used for training, validation, blind testing, and benchmarking of the
SPPIDER-seq partner-aware protein–protein interaction site prediction models.
For the software, documentation, and usage instructions, see the
[SPPIDER-seq GitHub repository](https://github.com/aporollo-lab/SPPIDER-seq).
For the current pretrained models, see the
[SPPIDER-seq model repository](https://huggingface.co/aporollo-lab/SPPIDER-seq).
Please cite the SPPIDER-seq publication when using these datasets:
> Porollo A, Jadhav O, Alvarez A, Chen J. **SPPIDER-seq: sequence-based partner-aware predictor of protein–protein interaction sites.** *Bioinformatics*. 2026;42(7):btag388. https://doi.org/10.1093/bioinformatics/btag388
---
## 1. Dataset prefixes and model usage
Files with different prefixes correspond to different model variants:
* Files starting with the prefix **`rec_`** were used for training, validation, and benchmarking of the **receptor-centric model**.
* Files starting with the prefix **`pep_`** were used for training, validation, and benchmarking of the **peptide-centric model**.
---
## 2. Pair definition files (`.tsv`)
Files with the `.tsv` extension define protein–peptide pairs used for different stages of model development:
* `*_train.tsv` — training dataset
* `*_val.tsv` — validation dataset used during training
* `*_blind.tsv` — blind benchmark dataset not seen during training or validation
Each `.tsv` file contains exactly two tab-separated columns:
1. `receptor_id` — identifier of the receptor sequence entry
2. `peptide_id` — identifier of the peptide or ligand sequence entry
Each row defines one receptor–peptide interaction pair. The corresponding full-length sequences and residue-level PPI annotations are provided in the associated ground-truth annotation files.
---
## 3. Sequence naming convention
Protein sequences in the `.tsv` files follow the naming convention:
```
PDBcode_ChainID|UniProtID|ChainPair
```
where:
* **PDBcode**
Indicates the PDB entry from which the interacting protein pair was derived.
* **ChainID**
Specifies the chain identifier corresponding to the sequence listed.
* **UniProtID**
Identifies the UniProt accession from which the full-length reference sequence was obtained.
* **ChainPair**
Describes the interaction context within the PDB complex.
The first chain ID always corresponds to the **receptor** chain, and the second chain ID corresponds to the **ligand (peptide)** chain.
If multiple chain pairs within the same PDB entry are identical in sequence and interaction context, they are listed as multiple `ChainPair` entries separated by the `=` character.
### Example protein–protein pairs
```
1ca9_A|Q12933|AG=EG 1ca9_G|P20333|AG=EG
1cg9_A|P01889|AC 1cg9_C|P03204|AC
1d8d_A|Q04631|AP 1d8d_P|P01116|AP
1d8d_B|Q02293|BP 1d8d_P|P01116|BP
1ddv_A|Q9Z214|AB 1ddv_B|P31424|AB
1ds5_A|P28523|AE=BE 1ds5_E|P67870|AE=BE
```
---
## 4. Ground-truth PPI site annotation files (`.txt`)
Files with the `.txt` extension contain residue-level ground-truth PPI site annotations derived from PDB structures.
Each protein entry consists of **four consecutive lines**:
1. **Header line**
Starts with the `>` character and contains the protein sequence name.
2. **Full-length sequence**
The complete protein sequence derived from the corresponding UniProt ID.
3. **PDB-derived sequence**
The protein sequence extracted from the PDB entry and specified chain, aligned to the full-length UniProt reference sequence.
Missing or unresolved residues are represented by `-` characters.
4. **Ground-truth PPI annotation**
A position-wise binary annotation indicating the PPI site state for each residue in the given interaction context (chain pair).
Interacting residues are marked with `1`, non-interacting residues with `0`.
### Example PPI site annotation entries
```
>1be3_K|P07552|JK
MLTRFLGPRYRQLARNWVPTASLWGAVGAVGLVWATDWRLILDWVPYINGKFKKDD
--------------RNWVPTAQLWGAVGAVGLVSAT--------------------
00000000000000010011001101100110010000000000000000000000
>1be3_J|P00130|JK
MVAPTLTARLYSLLFRRTSTFALTIVVGALFFERAFDQGADAIYEHINEGKLWKHIKHKYENKE
-VAPTLTARLYSLLFRRTSTFALTIVVGALFFERAFDQGADAIYEHINEGKLWKHIKHKYENK-
0000000000000000111101100110010000000000000000000000000000000000
>1vf5_G|P83797|BG
MVEPLLDGLVLGLVFATLGGLFYAAYQQYKRPNELGG
--------LVLGLVFATLGGLFYAAYQQYKR------
0000000000000110010011010011001000000
>1vf5_B|P83792|BG
MATLKKPDLSDPKLRAKLAKGMGHNYYGEPAWPNDLLYVFPVVIMGTFACIVALSVLDPAMVGEPADPFATPLEILPEWYLYPVFQILRSVPNKLLGVLLMASVPLGLILVPFIENVNKFQNPFRRPVATTIFLFGTLVTIWLGIGATFPLDKTLTLGLF
-----------------LAKGMGHNYYGEPAWPNDLLYVFPVVIMGTFACIVALSVLDPAMVGEPANPFATPLEILPEWYLYPVFQILRSLPNKLLGVLLMASVPLGLILVPFIENVNKFQNPFRRPVATTIFLFGTLVTIWLGIGAALPLDKTL-----
0000000000000000000000000000000100000010011001001100110010000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000
```
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