CovInter 2.0 now integrates over 61,000 molecular interactions across six major types. The comprehensive dataset is comprised of: 33,939 Virus Protein-Host Protein Interactions (VPHPIs) between 463 viral proteins (from 46 strains) and 7,555 host proteins (from 34 species); 13,763 Virus RNA-Host RNA Interactions (VRHRIs) between 288 viral RNAs (from 20 strains) and 8,597 host RNAs; and an expanded set of 12,837 Virus RNA-Host Protein Interactions (VRHPIs) linking 322 viral RNA regions to 1,825 host proteins. The database is completed by more specialized datasets, including 618 Virus Protein-Host RNA Interactions (VPHRIs), 542 Virus Protein-Virus Protein Interactions (VPVPIs) among 131 viral proteins, and 129 Virus RNA-Virus Protein Interactions (VRVPIs).

2. Search for Interactions by Virus RNA

2.1 Search by Virus Name

For example, if users want to know detailed information on the interaction with any of the SARS-CoV-2 RNA, 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 with any of the Coronavirus RNA regions, 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 with any of the coronavirus RNA strains, 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”, “Interactions Network”, “List of partners interacting with this Virus RNA”, “Virus RNA Sequence Information” and “References” information.

4. Search for Interactions by Virus protein

4.1 Search by Virus Protein Name

Virus protein related interactions can be searched by entering the protein name in the “search box” on the main page and in the “Search for virus protein entries” on the search page.

4.2 Search by Virus Strains

If users want to know detailed information on the interaction with any of strains the coronavirus proteins belong to, the user can search by selecting an organism and selecting a strain of this organism by “Search for virus protein entries” or “Search for protein entries by virus strain”.

4.3 Search by Virus Protein 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 this virus protein.

5. Detailed information on Virus Protein page

The virus protein page contains mainly “Virus Protein General information”, “Interactions Network”, “List of partners interacting with this virus protein”, “Protein Sequence Information”, and “References” information.

6. Search for Interactions by Host RNA

6.1 Search by Host RNA Name

Host RNA related interactions can be searched by entering the RNA name in the “search box” on the main page and in the “Search for host RNA entries” on the search page.

6.2 Search by Host Species

If users want to know detailed information on the interaction with any of host species the host RNA belongs to, the user can search by selecting a host species and selecting an RNA binding region of this speceis by “Search for host RNA entries” or “Search for host RNA entries by host species”.

6.3 Search by RNA Categories

Host RNA related interactions can be searched by selecting the category of RNA in the “search box” on the main page and in the “Search for host RNA entries by RNA categories” on the search page.

7. Detailed information on host RNA page

The host RNA page contains mainly “host RNA General information”, “Interactions Network”, “List of partners interacting with this host RNA”, “RNA Sequence Information” and “References” information.

8. Search for Interactions by Host protein

8.1 Search by host protein name

Host protein related interactions 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.

8.2 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.

8.3 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 selected host proteins.

9. Detailed information on the host protein page

By clicking the “Pro info” button, the detailed information page of this 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-Virus RNA Network”, “Different Gene Expression after Virus Infection”, “Protein Phosphorylation after Virus Infection”, “Potential Drugs Target Information of this Protein”,“Protein Sequence Information”, and “References”.

10. Browse page

First, you can choose one of these six kinds of interactions.Then,the browse page displays a list of all interaction-related information in the database. Click on “RNA info” or “Pro info” to see more detailed information.

11. Download the page

The Download page allows users to download all Full data from the database, including “Coronavirus interactions data Downloads”, “Coronavirus RNA associated with interaction Downloads”, “Coronavirus protein associated with interaction Downloads”, “Host proteins associated with interaction Downloads”,“Host RNA associated with interaction Downloads”, “KEGG pathways associated with infection Downloads”, “Different Gene Expression associated with virus infection Downloads”, “Phosphorylation sites of host protein associated with virus infection Downloads”and “Reference of CovInter Database”.