Seven types of coronaviruses were covered in CovInter which included SARS-CoV-2, SARS-CoV-1, MERS, HCoV-OC43, HCoV-NL63, HCoV-HKU1, and HCoV-229E. A total of 10,344 IVRHP data between 310 virus RNA regions and 1,281 host proteins were collected. For each host protein, detailed information was provided in CovInter, such as protein name, protein family, gene name, EC number, subcellular location, sequence, UniProt ID, gene ID, Ensembl ID, HGNC ID, and protein function. The 2D and 3D structures of these proteins from PDB, SWISS-MODEL, or AlphaFold were also displayed. For each coronavirus RNA, detailed information, including virus name, taxonomy ID, strains name, strains family, GISAID accession ID, strains mutation site, and predicted 2D structure by RNAfold were also provided. Moreover, for each IVRHP data pair, the experimental information including virus infection time, infection cells, cell-originated tissue, interaction detection methods, interaction type, and interaction binding type were explicitly recorded. All these interactions were validated in diverse living systems (including 30 cell lines from 14 tissue) and various model organisms.

2. Search for virus RNA-Host protein interactions by Virus RNA

2.1 Search by Virus Name

For example, if users want to know detailed information on the interaction between any of the SARS-CoV-2 RNA and host proteins, Users can search by entering a virus name in “The Search for Virus RNA Entries” box or by selecting a virus name in the “Search for Virus RNA Entries” box.

2.2 Search by Virus RNA Region

If users want to know detailed information on the interaction between any of the Coronavirus RNA regions and host proteins, users can search by clicking the different RNA regions on the main page, or Search for Virus RNA Entries: “by Virus Regions name on the Virus search page.”

2.3 Search by Virus strains

If users want to know detailed information on the interaction between any of the coronavirus RNA strains and host proteins, the user can search by selecting a strain and selecting a region of this strain by “Search for viral RNA entries” or “Search for viral RNA entries by strain name”.

2.4 Resulting webpage of Virus RNA

The resulting webpage displays profiles of all the strains regions and strains general information on “SARS-CoV-2”. By clicking the hyperlinks “Detail info” button, detailed information on SARS-CoV-2 strains regions and host protein interaction information can be recursively searched.

3. Detailed information on Virus RNA page

The virus RNA page contains mainly “Virus RNA General information”, “Virus RNA-Protein Network” and “Full list of protein interaction with this Virus Region” information.

4. Search for Virus RNA-Host Protein Interactions by Host Protein

4.1 Search by host protein name

Virus RNA-interacting host proteins can be searched by entering the protein name in the “search box” on the main page and in the “Search for protein entries” on the search page.

4.2 Search by KEGG pathways

In “Search for Protein Entries by KEGG Pathways”, select the name of a KEGG pathway, and then select the name of a protein related to this pathway.

4.3 Search by Subcellular localization

In “Search for Protein Entries by Protein Subcellular Localization”, select a cellular subcellular localization, and then select a related protein name.

The resulting web page shows detailed information on viral RNA interaction proteins.

5. Detailed information on the host protein page

By clicking the “Pro info” button, the detailed information page of this RNA interaction protein detailed information will be displayed. Details of Host Protein page contain mainly “Host protein general information”, Related “KEGG pathways” information, “Protein function during virus infection”, and “Virus RNA-host proteins regulation networks” information. The details page includes: “Host Protein General information”, “Protein Function in Virus Infection”, “Protein-VirusRNA Network”, “Full list of Virus RNA interaction with this Protein”, “Different Gene Expression after Virus Infection”, “Protein Phosphorylation after Virus Infection”, “Potential Drug Target Information of this Protein”, and “Protein Sequence Information”.

6. Brows page

The browse page displays a list of all virus RNA-host protein interaction-related information in the database. Click on “RNA info” or “Pro info” to see more detailed information about virus RNA and interaction protein.

7. Download the page

The Download page allows users to download all Full data from the database, including “The pair information of coronavirus RNA-host protein interactions”, “general information of coronavirus RNA”, “general information of protein associated with interaction”, “function of protein associated with interaction during infection”, “KEGG pathways related with infection”, “different gene expression before and after infection”.