DBCOVP: A database of coronavirus virulent glycoproteins

Abstract

Since the emergence of SARS-CoV-1 (2002), novel coronaviruses have emerged periodically like the MERS- CoV (2012) and now, the SARS-CoV-2 outbreak which has posed a global threat to public health. Although, this is the third zoonotic coronavirus breakout within the last two decades, there are only a few platforms that provide information about coronavirus genomes. None of them is specific for the virulence glycoproteins and complete sequence-structural features of these virulence factors across the betacoronavirus family including SARS-CoV-2 strains are lacking. Against this backdrop, we present DBCOVP (http://covp.immt.res.in/), the first manually-curated, web-based resource to provide extensive information on the complete repertoire of structural virulent glycoproteins from coronavirus genomes belonging to betacoronavirus genera. The database provides various sequence-structural properties in which users can browse and analyze information in different ways. Furthermore, many conserved T-cell and B-cell epitopes predicted for each protein are present that may perform a significant role in eliciting the humoral and cellular immune response. The tertiary structure of the epitopes together with the docked epitope-HLA binding-complex is made available to facilitate further analysis. DBCOVP presents an easy-to-use interface with in-built tools for similarity search, cross-genome comparison, phylogenetic, and multiple sequence alignment. DBCOVP will certainly be an important resource for experimental biologists engaged in coronavirus research studies and will aid in vaccine development.

Keywords: Bioinformatics; COVID-19; Coronavirus; Database; Glycoproteins; Immunoinformatics.

Fig. 1

Schematic representation of complete protocol employed for theidentification of promiscuous epitope-based vaccine candidates present in DBCOVP.

Fig. 2

Screenshot of DBCOVP Web-interface: a) ‘Advanced Search’ provides users to input multiple search queries simultaneously to retrieve specific proteins of interest. b) Browse by ‘Subgenus’, ‘Epitope’ and ‘Proteins’. c) Details page for a coronavirus strain d) Result page from Browse by ‘Subgenus’. e) The detailed annotation page of a protein.

Fig. 3

Detailed immunogenic information obtained for proteins using Browse by Epitope.

Fig. 4

Schematic representation of database content and annotation features: a) Summary tab of protein annotation page. b) Structural Details tab of protein annotation page. c) Physicochemical properties tab of protein annotation page. d) Epitopes tab of protein annotation page.