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The present study aimed to apply bioinformatic methods to analyze the structure of the S protein of human respiratory coronaviruses, including severe respiratory disease syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), human coronavirus HKU1 (HCoV-HKU1), and severe respiratory disease syndrome coronavirus type 2 (SARS-CoV-2). We predicted and analyzed the physicochemical properties, hydrophilicity and hydrophobicity, transmembrane regions, signal peptides, phosphorylation and glycosylation sites, epitopes, functional domains, and motifs of the S proteins of human respiratory coronaviruses. All four S proteins contain a transmembrane region, which enables them to bind to host cell surface receptors. All four S proteins contain a signal peptide, phosphorylation sites, glycosylation sites, and epitopes. The predicted phosphorylation sites might mediate S protein activation, the glycosylation sites might affect the cellular orientation of the virus, and the predicted epitopes might have implications for the design of antiviral inhibitors. The S proteins of all four viruses have two structural domains, S1 (C-terminal and N-terminal domains) and S2 (homology region 1 and 2). Our bioinformatic analysis of the structural and functional domains of human respiratory coronavirus S proteins provides a basis for future research to develop broad-spectrum antiviral drugs, vaccines, and antibodies.
Pubmed ID: 36657625
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Server that predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons. NetNGlyc 1.0 is also available as a stand-alone software package, with the same functionality as the service above. Ready-to-ship packages exist for the most common UNIX platforms.
View all literature mentionsNIH genetic sequence database that provides annotated collection of all publicly available DNA sequences for almost 280 000 formally described species (Jan 2014) .These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. It is part of International Nucleotide Sequence Database Collaboration and daily data exchange with European Nucleotide Archive (ENA) and DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through NCBI Entrez retrieval system, which integrates data from major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of GenBank database are available by FTP.
View all literature mentionsDatabase of protein families and domains that is based on the observation that, while there is a huge number of different proteins, most of them can be grouped, on the basis of similarities in their sequences, into a limited number of families. Proteins or protein domains belonging to a particular family generally share functional attributes and are derived from a common ancestor. It is complemented by ProRule, a collection of rules based on profiles and patterns, which increases the discriminatory power of profiles and patterns by providing additional information about functionally and/or structurally critical amino acids. ScanProsite finds matches of your protein sequences to PROSITE signatures. PROSITE currently contains patterns and profiles specific for more than a thousand protein families or domains. Each of these signatures comes with documentation providing background information on the structure and function of these proteins. The database is available via FTP.
View all literature mentionsServer that produces predictions of mucin-type GalNAc O-glycosylation sites in mammalian proteins.
View all literature mentionsSoftware for 3D/4D image reconstruction. UCSF ChimeraX is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.
View all literature mentionsSoftware tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity.
View all literature mentionsSoftware tool that extends WholeBrain framework in R for segmenting and registering experimental images to Allen Mouse Common Coordinate Framework (CCF). Streamlines processing of large volumetric LSFM datasets and solves issues with non-uniform morphing across anterior-posterior axis with interactive “choice game.” Accounts for duplicate cell counts in adjacent z images and presents new ways to easily parse apart and interactively visualize final mapped datasets.
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