Welcome to Interaction Database (IDB)

IDB is an open resource of mass spectrometry driven interaction database with data compiled through comprehensive curation efforts. IDB 1.1 currently holds 863,926 (745,163+118,763) interactions from individual focused studies through affinity purification coupled mass spectrometry (AP-MS). All data are available for download in our standardized format.

Signaling pathway interactome

In order to systematically explore the landscape of interactions among the seven signaling pathways (Hippo, MAPK, JAK-STAT, Notch, Hedgehog, TGF-β, Wnt), a total number of 120 known key component proteins were selected as the bait proteins to perform AP-MS experiments. In total, 118763 binary bait-prey interactions and 10470 unique preys were detected from the AP-MS experiments.

Minkowski distance-based unified scoring environment (MUSE)

MUSE is an adaptive-control method that identifies high confidence protein-protein interaction from AP-MS data. Further, we expanded MUSE, enabling it to identify pathway regulators and identify Inter-pathways hub proteins. This function also allows users to perform intra-group and inter-group analysis of their AP-MS data.

A comprehensive SARS-CoV-2-human protein interaction network

We conducted a comprehensive study of the interactome of the viral-host PPI networks of 44 SARS-CoV-2 proteins (including 29 WT SARS-CoV-2 proteins and 15 distinct S proteins of Alpha, Beta, Gamma, Delta, Kappa, Mu and Omicron BA.1, BA.2, BA.3, BA.4, BA.5, BF.7, BQ.1, BQ.1.1, XBB1.5 variants) in human lung-, bronchus-, neuron-, liver- and kidney-derived cells, which are susceptible to SARS-CoV-2 infection. In total, we performed 440 tandem affinity purification and mass spectrometry experiments and identified 221k unique peptides representing 739k viral-host PPIs.

Protein complex structure prediction

We predicted the structure of the SARS-CoV-2 S-host protein complexes using AlphaFold 3 and experimentally validated the functions of several complexes in mediating viral infection and replication.

Histidine Phosphorylation Project

Phosphorylation of serine, threonine and tyrosine is common in both prokaryotes and eukaryotes. Previous studies have suggested that histidine phosphorylation is a unique regulatory mode for prokaryotic proteins, and its main role is to transfer signals in cells through two-component or multi-component phosphorus delivery systems. However, the function of histidine phosphorylation in mammals is still not well understood and needs further investigation.

Publications supported by the MUSE

Jiang H, Bian W, Sui Y, Li H, Zhao H, Wang W, Li X. FBXO42 facilitates Notch signaling activation and global chromatin relaxation by promoting K63-linked polyubiquitination of RBPJ. Sci Adv. 2022 Sep 23;8(38):eabq4831. doi: 10.1126/sciadv.abq4831. Epub 2022 Sep 21. PMID: 36129980; PMCID: PMC9491713.

Bian W, Jiang H, Feng S, Chen J, Wang W, Li X. Protocol for establishing a protein-protein interaction network using tandem affinity purification followed by mass spectrometry in mammalian cells. STAR Protoc. 2022 Jul 19;3(3):101569. doi: 10.1016/j.xpro.2022.101569. PMID: 35874475; PMCID: PMC9304681.

Bian W, Tang M, Jiang H, Xu W, Hao W, Sui Y, Hou Y, Nie L, Zhang H, Wang C, Li N, Wang J, Qin J, Wu L, Ma X, Chen J, Wang W, Li X. Low-density-lipoprotein-receptor-related protein 1 mediates Notch pathway activation. Dev Cell. 2021 Oct 25;56(20):2902-2919.e8. doi: 10.1016/j.devcel.2021.09.015. Epub 2021 Oct 8. PMID: 34626540.

Wang S, Qiu Z, Hou Y, Deng X, Xu W, Zheng T, Wu P, Xie S, Bian W, Zhang C, Sun Z, Liu K, Shan C, Lin A, Jiang S, Xie Y, Zhou Q, Lu L, Huang J, Li X. AXL is a candidate receptor for SARS-CoV-2 that promotes infection of pulmonary and bronchial epithelial cells. Cell Res. 2021 Feb;31(2):126-140. doi: 10.1038/s41422-020-00460-y. Epub 2021 Jan 8. PMID: 33420426; PMCID: PMC7791157.

Vargas R, Duong V, Han H, Ta AP, Chen Y, Zhao S, Yang B, Seo G, Chuc K, Oh S, Razorenova O, Chen J*, Luo R*, Li X*, Wang W* (2020) Elucidation of WW domain ligand binding specificities in the Hippo pathway reveals STXBP4 as YAP inhibitor. EMBO Journal 39:e102406.

Seo G, Han H, Vargas R, Yang B, Li X*, Wang W* (2020) Proteomic analysis of the human MAP4Ks protein interaction network identifies STRIPAK complex component STRN4 as a negative regulator of the Hippo pathway. Cell Reports 32:107860.