Structure of covid19

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coviki.org collects the really good Ideas and the scientific Record on Covid-19 Virus.

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major items will be recollected into the pharmacophore section

PHA pharmacophore by screened target

integrative papers

32507543 2020. Spiking Pandemic Potential: Structural and Immunological Aspects of SARS-CoV-2.


32181901 ä. A guideline for homology modeling of the proteins from newly discovered betacoronavirus, 2019 novel coronavirus (2019?nCoV)
32296735 2020. Prudently conduct the engineering and synthesis of the SARS-CoV-2 virus
C7085496 ä. Structural, glycosylation and antigenic variation between 2019 novel coronavirus (2019-nCoV) and SARS coronavirus (SARS-CoV)
32254054 2020. Visualizing an unseen enemy; mobilizing structural biology to counter COVID-191
32311462 2020. On the molecular determinants of the SARS-CoV-2 attack
32229288 ä. Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy
32306836 2020. Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment
32265180 ä. Genotype and phenotype of COVID-19: Their roles in pathogenesis
32178970 2020. Composition of human-specific slow codons and slow di-codons in SARS-CoV and 2019-nCoV are lower than other coronaviruses suggesting a faster protein synthesis rate of SARS-CoV and 2019-nCoV
32350227 2020. Characteristics of SARS-CoV-2 isolated from asymptomatic carrier in Tokyo

32342926 2020. Properties of Coronavirus and SARS-CoV-2


32194253 ä. Molecular basis of COVID-19 relationships in different species: a one health perspective
C7085496 ä. Structural, glycosylation and antigenic variation between 2019 novel coronavirus (2019-nCoV) and SARS coronavirus (SARS-CoV)

32218151 2020. Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins


32098422 2020. Systematic Comparison of Two Animal-to-Human Transmitted Human Coronaviruses: SARS-CoV-2 and SARS-CoV

32348474 2020. Expanding our understanding of the role polyprotein conformation plays in the coronavirus life cycle


32367648 2020. SARS-CoV-2 variants: Relevance for symptom granularity, epidemiology, immunity (herd, vaccines), virus origin and containment?
32342578 2020. The Importance Of Naturally Attenuated Sars-Cov-2 In The Fight Against Covid-19
32104911 ä. Evolutionary history, potential intermediate animal host, and cross?species analyses of SARS?CoV?2
32365353 2020. Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform
32092385 2020. The continuous evolution and dissemination of 2019 novel human coronavirus
32361530 2020. The puzzle of sharing bio-molecular targets between coronaviruses and mediators of the cardiovascular system in humans: Looking for plausible hypotheses
32402329 2020. Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses
32452417 2020. New insights into the evolutionary features of viral overlapping genes by discriminant analysis

31916022 2020. Cryo-EM Studies of Virus-Antibody Immune Complexes


32558639 2020. Isolation, Sequence, Infectivity, and Replication Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2.
32592845 2020. Comparative analysis of protein synthesis rate in COVID-19 with other human coronaviruses.

32579100 2020. Insights into SARS-CoV-2, the Coronavirus Underlying COVID-19: Recent Genomic Data and the Development of Reverse Genetics Systems.


32598499 2020. SARS-CoV-2: march toward adaptation.

32536162 2020. Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses.


genome

32596428 2020. Data stream dataset of SARS-CoV-2 genome.


32543691 2020. Genetic Analysis Tracks SARS-CoV-2 Mutations in Human Hosts.


32595352 2020. An updated analysis of variations in SARS-CoV-2 genome.
32595351 2020. Phylogenetic analysis of SARS-CoV-2 genomes in Turkey.
32595958 2020. Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India.
32595354 2020. Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey.
32595356 2020. SARS-CoV-2 isolation and propagation from Turkish COVID-19 patients.
32596474 2020. Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2.
32543353 2020. SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East.
32543348 2020. Virus strain from a mild COVID-19 patient in Hangzhou represents a new trend in SARS-CoV-2 evolution potentially related to Furin cleavage site.
32586872 2020. Genome Sequence of SARS-CoV-2 Isolate Cali-01, from Colombia, Obtained Using Oxford Nanopore MinION Sequencing.
32581081 2020. Rampant C-->U Hypermutation in the Genomes of SARS-CoV-2 and Other Coronaviruses: Causes and Consequences for Their Short- and Long-Term Evolutionary Trajectories.
32566234 2020. Phyloevolutionary analysis of SARS-CoV-2 in Nigeria.
32571880 2020. Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2).

32605661 2020. Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples.


32610037 2020. Rapid, Sensitive, Full-Genome Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2.
32556599 2020. Full genome sequence of the first SARS-CoV-2 detected in Mexico.
32512089 2020. Corona virus versus existence of human on the earth: A computational and biophysical approach.
32528156 2020. Ten recommendations for supporting open pathogen genomic analysis in public health.
32509310 2020. Severe acute respiratory syndrome coronavirus 2: virus mutations in specific European populations.
32528815 2020. Genome-Wide Identification and Characterization of Point Mutations in the SARS-CoV-2 Genome.
32431949 2020. Multivariate analyses of codon usage of SARS-CoV-2 and other betacoronaviruses.
32509472 2020. Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions.

32512929 2020. The Prediction of miRNAs in SARS-CoV-2 Genomes: hsa-miR Databases Identify 7 Key miRs Linked to Host Responses and Virus Pathogenicity-Related KEGG Pathways Significant for Comorbidities.


32513865 2020. Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.
32450246 2020. Molecular epidemiology of SARS-CoV-2 in Faisalabad, Pakistan: A real-world clinical experience.
32292587 2020. Mutated COVID-19, May Foretells Mankind in a Great Risk in the Future.
32483490 2020. The role of selectivity of the SARS-CoV-2 virus for human genetic profiles in susceptibility and resistance to COVID-19.
32381617 2020. Near-Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Peru.
32467284 2020. Coding-Complete Genome Sequences of Two SARS-CoV-2 Isolates from Egypt.
32467283 2020. Complete Genome Sequence of SARS-CoV-2 in a Tiger from a U.S. Zoological Collection.
32409547 2020. Complete Genome Sequences of SARS-CoV-2 Strains Detected in Malaysia.
32527780 2020. Complete Genome Sequence of a Novel Coronavirus (SARS-CoV-2) Isolate from Bangladesh.
32528128 2020. Bat-borne virus diversity, spillover and emergence.
32464496 2020. Genetic variation in SARS-CoV-2 may explain variable severity of COVID-19.
32412415 2020. A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis.
32398273 2020. RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look.

32330414 ä. The Architecture of SARS-CoV-2 Transcriptome


32289263 ä. An Infectious cDNA Clone of SARS-CoV-2

32341946 2020. Chaos game representation dataset of SARS-CoV-2 genome


C7200767 2020. Chaos game representation dataset of SARS-CoV-2 genome
32301390 2020. Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction
32167166 ä. An exclusive 42 amino acid signature in pp1ab protein provides insights into the evolutive history of the 2019 novel human?pathogenic coronavirus (SARS?CoV?2)
32145215 ä. Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2
32471829 2020. Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis of SARS-CoV-2-Related Viruses.
32437232 2020. Virus-induced genetics revealed by multidimensional precision medicine transcriptional workflow applicable to COVID-19.
32422894 2020. A Novel Synonymous Mutation of SARS-CoV-2: Is This Possible to Affect Their Antigenicity and Immunogenicity?

32484220 2020. Discovery of G-quadruplex-forming sequences in SARS-CoV-2.


32472763 2020. Comparative analysis of Coronaviridae nucleocapsid and surface glycoprotein sequences.
32474553 2020. Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type.
32492196 2020. High-Coverage SARS-CoV-2 Genome Sequences Acquired by Target Capture Sequencing.
32492183 2020. Evidence for mutations in SARS-CoV-2 Italian isolates potentially affecting virus transmission.

32420944 2020. The impact of MicroRNAs (miRNAs) on the genotype of coronaviruses.
32425659 2020. Investigating the genomic landscape of novel coronavirus (2019-nCoV) to identify non-synonymous mutations for use in diagnosis and drug design.
32522874 2020. Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses.


32416074 2020. A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein.
32525765 2020. Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries.
32524946 2020. Genetic structure of SARS-CoV-2 reflects clonal superspreading and multiple independent introduction events, North-Rhine Westphalia, Germany, February and March 2020.

32473977 2020. Unfolding SARS-CoV-2 viral genome to understand its gene expression regulation.


32501423 2020. Developing an ultra-efficient microsatellite discoverer to find structural differences between SARS-CoV-1 and Covid-19.

structure


32092911 2020. Rigidity of the Outer Shell Predicted by a Protein Intrinsic Disorder Model Sheds Light on the COVID-19 (Wuhan-2019-nCoV) Infectivity

32362648 2020. Transmission electron microscopy imaging of SARS-CoV-2


32292212 2020. Photopolarimetrical properties of coronavirus model particles: Spike proteins number influence
32470119 2020. Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence.

32493627 2020. Structural Proteins in Severe Acute Respiratory Syndrome Coronavirus-2.
32446936 2020. Electron Microscopic Investigations in COVID-19: Not all Crowns Are Coronas.
renal virus-like structures are normal cell constituents


32442529 2020. Electron microscopy of SARS-CoV-2: a challenging task. img of read viral particles
32442527 2020. Electron microscopy of SARS-CoV-2: a challenging task - Authors' reply.
32455617 2020. Novel Dynamic Structures of 2019-nCoV with Nonlocal Operator via Powerful Computational Technique.
32470223 2020. COVID-19: Structural Predictions of Viral Success.


all the proteins

32447571 2020. The Proteins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2 or n-COV19), the Cause of COVID-19.


32462744 2020. Shortlisting SARS-CoV-2 Peptides for Targeted Studies from Experimental Data-Dependent Acquisition Tandem Mass Spectrometry Data.
32083638 2020. Processing of the SARS-CoV pp1a/ab nsp7-10 region.
32596311 2020. Sars-CoV-2 Envelope and Membrane Proteins: Structural Differences Linked to Virus Characteristics?
32604797 2020. Data and Text Mining Help Identify Key Proteins Involved in the Molecular Mechanisms Shared by SARS-CoV-2 and HIV-1.

primase complex

32535228 2020. Structural analysis of the putative SARS-CoV-2 primase complex.

nsp

32270884 2020. Role of Nonstructural Proteins in the Pathogenesis of SARS-CoV-2


32275073 2020. Response to Ribeiro da Silva et al ,"Role of Nonstructural Proteins in the Pathogenesis of SARS-CoV-2

nsp1 protein

PHA SCR nsp1

nsp2 protein

PHA SCR nsp2

nsp3 protein

PHA SCR nsp3

nsp6 protein

PHA SCR nsp6

nsp7b


32142938 2020. Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV

nsp8


32142938 2020. Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated with evolution of 2019-nCoV

nsp9


32592996 2020. Crystal Structure of the SARS-CoV-2 Non-structural Protein 9, Nsp9.

nsp10, nsp16 methyltransferase

PHA SCR nsp10 nsp16 methyltransferase

nsp13 protein NTPase, RNA helicase

PHA SCR nsp13 helicase, nucleotidase

nsp14

PHA SCR nsp14

nsp15 endoribonuclease NendoU

PHA SCR nsp15 endoribonuclease

papain-like proteinase

PHA SCR papain-like proteinase

replication factors, nsp12, nsp8, nsp7

PHA SCR rna-dependent rna-polymerase

nucleocapsid


32363136 ä. Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites
32302675 ä. Comparative computational analysis of SARS-CoV-2 nucleocapsid protein epitopes in taxonomically related coronaviruses
32416961 2020. Biochemical characterization of SARS-CoV-2 nucleocapsid protein

32291557 ä. SARS-CoV-2-encoded nucleocapsid protein acts as a viral suppressor of RNA interference in cells
32562316 2020. A proposed role for the SARS-CoV-2 nucleocapsid protein in the formation and regulation of biomolecular condensates.
32589897 2020. The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway.


vacuolar interaction

32485205 2020. The endosomal lipid bis(monoacylglycero) phosphate as a potential key player in the mechanism of action of chloroquine against SARS-COV-2 and other enveloped viruses hijacking the endocytic pathway.


innate interference

virus secretion

envelope
32446902 2020. Immunoinformatic analysis of the SARS-CoV-2 envelope protein as a strategy to assess cross-protection against COVID-19.


receptor binding any target

32565603 2020. Update on the target structures of SARS-CoV-2: A systematic review.


32604730 2020. SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus-Host Interaction.
32595513 2020. New Strategy for COVID-19: An Evolutionary Role for RGD Motif in SARS-CoV-2 and Potential Inhibitors for Virus Infection.

receptor binding: trmpss2

PHA SCR spike protein TMPRSS2

receptor binding: trmpss4

PHA SCR spike protein TMPRSS4

receptor binding: grp78, g-proteins

PHA SRC spike protein Grp78

candidate receptor binding DPP4


32405622 2020. The MERS-CoV Receptor DPP4 as a Candidate Binding Target of the SARS-CoV-2 Spike.

Uptake: cathepsin L

PHA SCR spike protein Cathepsin L

endocytosis membrane fusion


32047258 ä. Fusion mechanism of 2019-nCoV and fusion inhibitors targeting HR1 domain in spike protein
32265513 ä. SARS-CoV-2 infects T lymphocytes through its spike protein-mediated membrane fusion
32130973 2020. A potential role for integrins in host cell entry by SARS-CoV-2
32246503 ä. SARS?COV?2 and infectivity: Possible increase in infectivity associated to integrin motif expression

32272173 2020. Coronavirus membrane fusion mechanism offers a potential target for antiviral development


32094589 ä. Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses

32376634 2020. Cell entry mechanisms of SARS-CoV-2


32047128 2020. Distinct Roles for Sialoside and Protein Receptors in Coronavirus Infection

32428379 2020. Understanding SARS-CoV-2 endocytosis for COVID-19 drug repurposing.


32479856 2020. SARS-CoV-2 entry in host cells-multiple targets for treatment and prevention.


3CL proteinase and main proteinase is the same

PHA SCR main protease

orf


32357959 2020. An 81 nucleotide deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020)
32371472 2020. SARS-CoV-2 and ORF3a: Nonsynonymous Mutations, Functional Domains, and Viral Pathogenesis
32433742 2020. Extended ORF8 Gene Region Is Valuable in the Epidemiological Investigation of SARS-similar Coronavirus.
32555321 2020. The ORF3a protein of SARS-CoV-2 induces apoptosis in cells.
32589897 2020. The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway.
32540495 2020. Molecular conservation and differential mutation on ORF3a gene in Indian SARS-CoV2 genomes.
32504060 2020. Immune evasion via SARS-CoV-2 ORF8 protein?


varia

32452762 2020. SARS-CoV-2 strategically mimics proteolytic activation of human ENaC.


32200634 ä. Protein Structure and Sequence Reanalysis of 2019-nCoV Genome Refutes Snakes as Its Intermediate Host and the Unique Similarity between Its Spike Protein Insertions and HIV-1

32289821 ä. Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense


32123347 ä. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2
C7152894 ä. A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES
32366025 2020. Codon Usage and Phenotypic Divergences of SARS-CoV-2 Genes
32291894 2020. Cytosine drives evolution of SARS-CoV-2
32159237 ä. From SARS and MERS CoVs to SARS?CoV?2: Moving toward more biased codon usage in viral structural and nonstructural genes
32387562 2020. Coding potential and sequence conservation of SARS-CoV-2 and related animal viruses
32294518 2020. A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses

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