aporollo-lab/SPPIDER-seq-datasets

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.

For the current pretrained models, see the SPPIDER-seq model repository.

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

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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.

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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.

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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

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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