Corpus overview


MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinE (4)

ProteinS (2)

ProteinM (2)

ORF3a (1)

ORF6 (1)


SARS-CoV-2 Proteins
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    Evolutionary Insights into the Envelope Protein HGNC Envelope Protein PROTEIN of SARS-CoV-2

    Authors: M. Shaminur Rahman; M. Nazmul Hoque; M. Rafiul Islam; Israt Islam; Israt Dilruba Mishu; Md. Mizanur Rahaman; Munawar Sultana; M. Anwar Hossain

    id:10.20944/preprints202008.0665.v1 Date: 2020-08-30 Source:

    The ongoing mutations in the structural proteins of SARS-CoV-2 is the major impediment for prevention and control of the COVID-19 MESHD disease. The envelope (E) protein PROTEIN of SARS-CoV-2 is a structural protein existing in both monomeric and homopentameric forms, associated with a multitude of functions including virus assembly, replication, dissemination, release of virions, infection, pathogenesis, and immune response stimulation. In the present study, 81,818 high quality E protein PROTEIN sequences retrieving from the GISAID were subjected to mutational analyses. Our analysis revealed that only 0.012 % (982/81818) stains possessed amino acid (aa) substitutions in 63 sites of the genome while 58.77% mutations in the primary structure of nucleotides in 134 sites. We found the V25A mutation in the transmembrane domain which is a key factor for the homopentameric conformation of E protein PROTEIN. We also observed a triple cysteine motif harboring mutations (L39M, A41S, A41V, C43F, C43R, C43S, C44Y, N45R) which may hinder the binding of E protein PROTEIN with spike glycoprotein PROTEIN. These results therefore suggest the continuous monitoring of each structural protein of SARS-CoV-2 since the number of genome sequences from across the world are continuously increasing.

    In silico Proteome analysis of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)

    Authors: Chittaranjan Baruah; Papari Devi; Dhirendra K Sharma

    doi:10.1101/2020.05.23.104919 Date: 2020-05-24 Source: bioRxiv

    Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (2019-nCoV), is a positive-sense, single-stranded RNA coronavirus. The virus is the causative agent of coronavirus disease 2019 MESHD ( COVID-19 MESHD) and is contagious through human-to-human transmission. The present study reports sequence analysis, complete coordinate tertiary structure prediction and in silico sequence-based and structure-based functional characterization of full SARS-CoV-2 proteome based on the NCBI reference sequence NC_045512 (29903 bp ss-RNA) which is identical to GenBank entry MN908947 and MT415321. The proteome includes 12 major proteins namely orf1ab polyprotein (includes 15 proteins), surface glycoprotein, ORF3a PROTEIN protein, envelope PROTEIN envelope protein HGNC, membrane glycoprotein PROTEIN, ORF6 PROTEIN protein, ORF7a PROTEIN protein, orf7b, ORF8 PROTEIN, Nucleocapsid phosphoprotein and ORF10 PROTEIN protein. Each protein of orf1ab polyprotein group has been studied separately. A total of 25 polypeptides have been analyzed out of which 15 proteins are not yet having experimental structures and only 10 are having experimental structures with known PDB IDs MESHD. Out of 15 newly predicted structures six (6) were predicted using comparative modeling and nine (09) proteins having no significant similarity with so far available PDB structures were modeled using ab-initio modeling. Structure verification using recent tools QMEANDisCo 4.0.0 and ProQ3 for global and local (per-residue) quality estimates indicate that the all-atom model of tertiary structure of high quality and may be useful for structure-based drug designing targets. The study has identified nine major targets ( spike protein PROTEIN, envelop protein, membrane protein, nucleocapsid PROTEIN protein, 2-O-ribose methyltransferase, endoRNAse, 3-to-5 exonuclease, RNA-dependent RNA polymerase PROTEIN and helicase HGNC) for which drug design targets could be considered. There are other 16 nonstructural proteins PROTEIN (NSPs), which may also be percieved from the drug design angle. The protein structures have been deposited to ModelArchive. Tunnel analysis revealed the presence of large number of tunnels in NSP3 HGNC NSP3 PROTEIN, ORF 6 protein and membrane glycoprotein PROTEIN indicating a large number of transport pathways for small ligands influencing their reactivity.

    Pharmaceutical Targeting the Envelope Protein PROTEIN of SARS-CoV-2: the Screening for Inhibitors in Approved Drugs

    Authors: Anatoly Chernyshev

    doi:10.26434/chemrxiv.12286421.v1 Date: 2020-05-14 Source: ChemRxiv

    An essential overview of the biological role of coronavirus viroporin ( envelope protein HGNC envelope protein PROTEIN) is given, together with the effect of its known inhibitors on the life cycle of coronavirus. A docking study is conducted using a set of known drugs approved worldwide (ca. 6000 compounds) on a structure of the SARS-CoV-2 viroporin modelled from the published NMR-resolved structures. The screening has identified 36 promising drugs currently on the market, which could be proposed for pre-clinical trials.

    Structural modeling and conserved epitopes prediction against SARS-COV-2 structural proteins for vaccine development

    Authors: Muhammad Tahir ul Qamar; Farah Shahid; Usman Ali Ashfaq; Sidra Aslam; Israr Fatima; Muhammad Mazhar Fareed; Ali Zohaib; Ling-Ling Chen

    doi:10.21203/rs.2.23973/v1 Date: 2020-02-18 Source: ResearchSquare

    Background: Coronavirus disease 2019 MESHD ( COVID-19 MESHD) caused by Severe Acute Respiratory Syndrome MESHD Corona virus 2 (SARS-COV-2) was first diagnosed in December 2019, Wuhan, China. Little is known about this new virus and it has the potential to cause severe illness and pneumonia MESHD in some people, therefore the development of an effective vaccine is highly desired.Methods: Immunoinformatics and statistical approaches were used in this study to forecast B- and T- cell epitopes for the SARS-COV-2 structural proteins (Surface glycoprotein, Envelope protein PROTEIN Envelope protein HGNC, and Membrane glycoprotein PROTEIN) that may play a key role in eliciting immune response against COVID-19 MESHD. Different types of B cell epitopes (linear as well as discontinuous) and T cell (MHC class I and MHC class II) were determined. Moreover, their antigenicity and allergenicity were also estimated.Results: The antigenic B-cell epitopes exposed to the outer surface were screened out and 23 linear B cell epitopes were selected. “SPTKLNDLCFTNVY” had the highest antigenicity score among B cell epitopes. The T-cell epitopes bound to multiple alleles, antigenic, non-allergen, non-toxic, and conserved in the protein sequence were shortlisted. In total, 16 epitopes (9 from MHC class I and 7 from MHC class II) were selected. Among the T-cell epitopes, MHC class I (IPFAMQMAYRFN) and MHC class II (VTLACFVLAAVYRIN) were classified as strongly antigenic. Digestion analysis verified the safety and stability of the peptides predicted during this study. Furthermore, docking analyses of predicted peptides showed significant interactions with the HLA-B7 allele.Conclusion: The putative antigen epitopes identified in this study may serve as vaccine candidates and can help to eliminate/control growing health threat of COVID-19 MESHD.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins

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