Databases

AASIA (Agricultural Animals Structural Interactome Atlas), the first comprehensive and structure-informed interactome database tailored to agricultural animals. AASIA features 410,382 high-confidence predicted PPIs across five agricultural animals, Gallus gallus (chicken), Anas platyrhynchos (duck), Sus scrofa (pig), Bos taurus (cattle) and Ovis aries (sheep), with nearly all interactions paired with corresponding 3D complex structures predicted by ESMFold.

Maintained by Jiajun Li

PlaASDB is a comprehensive plant-specific AS database that mainly integrates the AS and gene expression data of Arabidopsis and rice in stress response. Through large-scale comparative analyses, the global landscape of AS events in Arabidopsis and rice was observed.

Maintained by Xiaokun Guo

HVIDB is a comprehensive database for human-virus protein-protein interactions. Currently, HVIDB highlights 48643 experimentally verified human–virus PPIs covering 35 virus families, 6633 virally targeted host complexes, 3572 host dependency/restriction factors as well as 911 experimentally verified/predicted 3D complex structures of human–virus PPIs. Furthermore, our database resource provides tissue-specific expression profiles of 6790 human genes that are targeted by viruses and 129 Gene Expression Omnibus series of differentially expressed genes post-viral infections. In addition, HVIDB also integrates well-performing machine learning models to predict interactions between the human host and viral proteins.

Maintained by Xiaodi Yang

PlaPPISite is a comprehensive, high-coverage and interaction details-oriented database for 13 plant interactomes. In addition to collecting 121 experimentally verified structures of protein complexes, the complex structures of experimental/predicted PPIs in the 13 plants were also constructed, and the corresponding interaction sites were annotated. For the PPIs whose 3D structures could not be modelled, the associated domain-domain interactions (DDIs) and domain-motif interactions (DMIs) were inferred. To facilitate the reliability assessment of predicted PPIs, the source species of interolog templates, GO annotations, subcellular localizations and gene expression similarities are also provided.

Maintained by Xiaodi Yang

PlaD is a transcriptomics database for plant defense responses to pathogens. PlaD contains 2444 public gene expression samples from 94 plant pathology-related studies, covering four important plants (Arabidopsis thaliana, Oryza sativa, Triticum aestivum and Zea mays). Each sample was manually curated based on plant tissues, pathogen types and infection stages. All the samples were consistently normalized and the fold change of differential expression was calculated for 522 conditions.

Maintained by Huan Qi

AraPPISite is an integrated database presenting fine-grained protein-protein interaction site annotations for Arabidopsis thaliana.

Maintained by Shiping Yang

Ralstonia solanacearum is a plant pathogen which can infect an unusually wide range of hosts. This bacterium and its host Arabidopsis thaliana have become a model system for studying the molecular basis of plant-pathogen interactions. For any phytopathogenic, protein-protein interactions (PPIs) play very important roles in infecting hosts. PPIs between R. solancearum and A. thaliana were constructed by two bioinformatic methods, the interolog and domain-based methods. The predicted PPIs were compiled as a PPI network called PPIRA, which contains 3074 PPIs between R. solancearum and A. thaliana.

Maintained by Zhigang Li

Bacterial Effector Analyzer 2.0 (BEAN 2.0) is an integrative web resource for prediction, analysis and storing type-III effectors.

Maintained by Xiaobao Dong