Data

Trained Models

Human PPI models trained on the cross-species dataset

• 650M model

  danliu1226/PLM-interact-650M-humanV11

• 35M model

  danliu1226/PLM-interact-35M-humanV11

Human PPI model trained on the Bernett dataset

• danliu1226/PLM-interact-650M-Leakage-Free-Dataset

Human PPI model trained on the STRING V12 training dataset

• danliu1226/PLM-interact-650M-humanV12

Virus-human PPI model

• danliu1226/PLM-interact-650M-VH

Mutation effect model

• danliu1226/PLM-interact-650M-Mutation

Pre-trained models can be downloaded from Hugging Face.

Datasets for PLM-interact

• Cross-species dataset

• Bernett dataset

• Mutation effect dataset

• Virus-human PPI dataset

• STRING V12 training dataset

Original Datasets

• Cross-species dataset[1]

• Bernett dataset[2]

• Mutation effect dataset[3]

• Virus-human PPI dataset[4]

• STRING V12 training dataset[5]

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).