Data
====

Trained Models
--------------
Human PPI models trained on the cross-species dataset 

- 650M model
    `danliu1226/PLM-interact-650M-humanV11 <https://huggingface.co/danliu1226/PLM-interact-650M-humanV11>`_

- 35M model
    `danliu1226/PLM-interact-35M-humanV11 <https://huggingface.co/danliu1226/PLM-interact-35M-humanV11>`_

Human PPI model trained on the Bernett dataset 

- `danliu1226/PLM-interact-650M-Leakage-Free-Dataset <https://huggingface.co/danliu1226/PLM-interact-650M-Leakage-Free-Dataset>`_ 

Human PPI model trained on the STRING V12 training dataset 

- `danliu1226/PLM-interact-650M-humanV12 <https://huggingface.co/danliu1226/PLM-interact-650M-humanV12>`_ 

Virus-human PPI model 

- `danliu1226/PLM-interact-650M-VH <https://huggingface.co/danliu1226/PLM-interact-650M-VH>`_ 

Mutation effect model 

- `danliu1226/PLM-interact-650M-Mutation <https://huggingface.co/danliu1226/PLM-interact-650M-Mutation>`_ 

Pre-trained models can be downloaded from `Hugging Face <https://huggingface.co/danliu1226>`_.

Datasets for PLM-interact
--------------------------
- `Cross-species dataset <https://huggingface.co/datasets/danliu1226/cross_species_benchmarking>`_
- `Bernett dataset <https://huggingface.co/datasets/danliu1226/Bernett_benchmarking>`_
- `Mutation effect dataset <https://huggingface.co/datasets/danliu1226/Mutation_effect_dataset>`_
- `Virus-human PPI dataset <https://huggingface.co/datasets/danliu1226/virus_human_benchmarking>`_
- `STRING V12 training dataset <https://huggingface.co/datasets/danliu1226/STRING_V12_TrainingSet>`_


Original Datasets
------------------
- `Cross-species dataset[1] <https://github.com/samsledje/D-SCRIPT/blob/main/data/>`_
- `Bernett dataset[2] <https://doi.org/10.6084/m9.figshare.21591618.v3>`_
- `Mutation effect dataset[3] <https://ftp.ebi.ac.uk/pub/databases/intact/current/various/mutations.tsv>`_
- `Virus-human PPI dataset[4] <http://kurata35.bio.kyutech.ac.jp/LSTM-PHV/download_page>`_
- `STRING V12 training dataset[5] <https://stringdb-downloads.org/download/protein.physical.links.v12.0.txt.gz>`_

References
-----------
[1] Sledzieski, S., Singh, R., Cowen, L. & Berger, B. D-SCRIPT translates genome to phenome with sequence-based, structure-aware, genome-scale predictions of protein-protein interactions. Cell Systems 12, 969-982.e6 (2021). 

[2] BBernett, J., Blumenthal, D. B. & List, M. Cracking the black box of deep sequence-based protein–protein interaction prediction. Briefings in Bioinformatics 25, bbae076 (2024). 

[3] Kerrien, S. et al. The IntAct molecular interaction database in 2012. Nucleic Acids Research 40, D841–D846 (2012).

[4]Tsukiyama, S., Hasan, M. M., Fujii, S. & Kurata, H. LSTM-PHV: prediction of human-virus protein–protein interactions by LSTM with word2vec. Briefings in Bioinformatics 22, bbab228 (2021). 

[5] Szklarczyk, D. et al. The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest. Nucleic Acids Research 51, D638–D646 (2023).