Structure of covid19

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__NOTOC__
'''general aspects'''
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===integrative papers===
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{{ttp|p=32507543|t=2020. Spiking Pandemic Potential: Structural and Immunological Aspects of SARS-CoV-2.|pdf=|usr=007}}
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{{tp|p=32181901|t=ä. A guideline for homology modeling of the proteins from newly discovered betacoronavirus, 2019 novel coronavirus (2019?nCoV) |pdf=|usr=}}
 +
{{tp|p=32296735|t=2020. Prudently conduct the engineering and synthesis of the SARS-CoV-2 virus |pdf=|usr=}}
 +
{{tp|p=C7085496|t=ä. Structural, glycosylation and antigenic variation between 2019 novel coronavirus  (2019-nCoV) and SARS coronavirus (SARS-CoV) |pdf=|usr=}}
 
{{tp|p=32254054|t=2020. Visualizing an unseen enemy; mobilizing structural biology to counter COVID-191 |pdf=|usr=}}
 
{{tp|p=32254054|t=2020. Visualizing an unseen enemy; mobilizing structural biology to counter COVID-191 |pdf=|usr=}}
{{tp|p=32254048|t=2020. Visualizing an unseen enemy; mobilizing structural biology to counter COVID-191 |pdf=|usr=}}
+
{{tp|p=32311462|t=2020. On the molecular determinants of the SARS-CoV-2 attack |pdf=|usr=}}
{{tp|p=32092911|t=2020. Rigidity of the Outer Shell Predicted by a Protein Intrinsic Disorder Model Sheds Light on the COVID-19 (Wuhan-2019-nCoV) Infectivity |pdf=|usr=}}
+
{{tp|p=32229288|t=ä. Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy |pdf=|usr=}}
{{tp|p=32330414|t=ä. The Architecture of SARS-CoV-2 Transcriptome |pdf=|usr=}}
+
{{tp|p=32306836|t=2020. Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment |pdf=|usr=}}
 +
{{tp|p=32265180|t=ä. Genotype and phenotype of COVID-19: Their roles in pathogenesis |pdf=|usr=}}
 +
{{tp|p=32178970|t=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 |pdf=|usr=}}
 +
{{tp|p=32350227|t=2020. Characteristics of SARS-CoV-2 isolated from asymptomatic carrier in Tokyo |pdf=|usr=}}
 +
{{ttp|p=32342926|t=2020. Properties of Coronavirus and SARS-CoV-2 |pdf=|usr=}}
 +
{{tp|p=32194253|t=ä. Molecular basis of COVID-19 relationships in different species: a one health perspective |pdf=|usr=}}
 +
{{tp|p=C7085496|t=ä. Structural, glycosylation and antigenic variation between 2019 novel coronavirus  (2019-nCoV) and SARS coronavirus (SARS-CoV) |pdf=|usr=}}
 +
{{ttp|p=32218151|t=2020. Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins |pdf=|usr=}}
 +
{{tp|p=32098422|t=2020. Systematic Comparison of Two Animal-to-Human Transmitted Human Coronaviruses: SARS-CoV-2 and SARS-CoV |pdf=|usr=}}
 +
{{ttp|p=32348474|t=2020. Expanding our understanding of the role polyprotein conformation plays in the coronavirus life cycle |pdf=|usr=}}
 +
{{tp|p=32367648|t=2020. SARS-CoV-2 variants: Relevance for symptom granularity, epidemiology, immunity (herd, vaccines), virus origin and containment?|pdf=|usr=}}
 +
{{tp|p=32342578|t=2020. The Importance Of Naturally Attenuated Sars-Cov-2 In The Fight Against Covid-19 |pdf=|usr=}}
 +
{{tp|p=32104911|t=ä. Evolutionary history, potential intermediate animal host, and cross?species analyses of SARS?CoV?2 |pdf=|usr=}}
 +
{{tp|p=32365353|t=2020. Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform |pdf=|usr=}}
 +
{{tp|p=32092385|t=2020. The continuous evolution and dissemination of 2019 novel human coronavirus |pdf=|usr=}}
 +
{{tp|p=32361530|t=2020. The puzzle of sharing bio-molecular targets between coronaviruses and mediators of the cardiovascular system in humans: Looking for plausible hypotheses |pdf=|usr=}}
 +
{{tp|p=32402329|t=2020. Novel human coronavirus (SARS-CoV-2): A lesson from animal coronaviruses |pdf=|usr=}}
 +
{{tp|p=32452417|t=2020. New insights into the evolutionary features of viral overlapping genes by discriminant analysis |pdf=|usr=}}
 +
{{ttp|p=31916022|t=2020. Cryo-EM Studies of Virus-Antibody Immune Complexes |pdf=|usr=}}
 +
{{tp|p=32558639|t=2020. Isolation, Sequence, Infectivity, and Replication Kinetics of Severe Acute Respiratory Syndrome Coronavirus 2.|pdf=|usr=010}}
 +
{{tp|p=32592845|t=2020. Comparative analysis of protein synthesis rate in COVID-19 with other human coronaviruses.|pdf=|usr=010}}
 +
{{ttp|p=32579100|t=2020. Insights into SARS-CoV-2, the Coronavirus Underlying COVID-19: Recent Genomic Data and the Development of Reverse Genetics Systems.|pdf=|usr=010}}
 +
{{tp|p=32598499|t=2020. SARS-CoV-2: march toward adaptation.|pdf=|usr=011}}
 +
{{ttp|p=32536162|t=2020. Role of RNA Guanine Quadruplexes in Favoring the Dimerization of SARS Unique Domain in Coronaviruses.|pdf=|usr=011}}
 +
 
 +
 
 +
===genome===
 +
*[[Genome announcements]] pure genome data without specific hypothesis
 +
*[[Interkingdom homologies]]
 +
{{ttp|p=32596428|t=2020. Data stream dataset of SARS-CoV-2 genome.|pdf=|usr=011}}
 +
{{tp|p=32543691|t=2020. Genetic Analysis Tracks SARS-CoV-2 Mutations in Human Hosts.|pdf=|usr=011}}
 +
 
 +
{{tp|p=32595352|t=2020. An updated analysis of variations in SARS-CoV-2 genome.|pdf=|usr=011}}
 +
{{tp|p=32595351|t=2020. Phylogenetic analysis of SARS-CoV-2 genomes in Turkey.|pdf=|usr=011}}
 +
{{tp|p=32595958|t=2020. Analyses of spike protein from first deposited sequences of SARS-CoV2 from West Bengal, India.|pdf=|usr=011}}
 +
{{tp|p=32595354|t=2020. Identification of the nucleotide substitutions in 62 SARS-CoV-2 sequences from Turkey.|pdf=|usr=011}}
 +
{{tp|p=32595356|t=2020. SARS-CoV-2 isolation and propagation from Turkish COVID-19 patients.|pdf=|usr=011}}
 +
{{tp|p=32596474|t=2020. Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2.|pdf=|usr=011}}
 +
{{tp|p=32543353|t=2020. SARS-CoV-2 genomic surveillance in Taiwan revealed novel ORF8-deletion mutant and clade possibly associated with infections in Middle East.|pdf=|usr=010}}
 +
{{tp|p=32543348|t=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.|pdf=|usr=010}}
 +
{{tp|p=32586872|t=2020. Genome Sequence of SARS-CoV-2 Isolate Cali-01, from Colombia, Obtained Using Oxford Nanopore MinION Sequencing.|pdf=|usr=010}}
 +
{{tp|p=32581081|t=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.|pdf=|usr=010}}
 +
{{tp|p=32566234|t=2020. Phyloevolutionary analysis of SARS-CoV-2 in Nigeria.|pdf=|usr=011}}
 +
{{tp|p=32571880|t=2020. Structural and functional conservation of the programmed -1 ribosomal frameshift signal of SARS coronavirus 2 (SARS-CoV-2).|pdf=|usr=011}}
 +
{{ttp|p=32605661|t=2020. Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples.|pdf=|usr=011}}
 +
{{tp|p=32610037|t=2020. Rapid, Sensitive, Full-Genome Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2.|pdf=|usr=011}}
 +
{{tp|p=32556599|t=2020. Full genome sequence of the first SARS-CoV-2 detected in Mexico.|pdf=|usr=010}}
 +
{{tp|p=32512089|t=2020. Corona virus versus existence of human on the earth: A computational and biophysical approach.|pdf=|usr=007}}
 +
{{tp|p=32528156|t=2020. Ten recommendations for supporting open pathogen genomic analysis in public health.|pdf=|usr=008}}
 +
{{tp|p=32509310|t=2020. Severe acute respiratory syndrome coronavirus 2: virus mutations in specific European populations.|pdf=|usr=009}}
 +
{{tp|p=32528815|t=2020. Genome-Wide Identification and Characterization of Point Mutations in the SARS-CoV-2 Genome.|pdf=|usr=009}}
 +
{{tp|p=32431949|t=2020. Multivariate analyses of codon usage of SARS-CoV-2 and other betacoronaviruses.|pdf=|usr=009}}
 +
{{tp|p=32509472|t=2020. Insights on early mutational events in SARS-CoV-2 virus reveal founder effects across geographical regions.|pdf=|usr=009}}
 +
{{ttp|p=32512929|t=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.|pdf=|usr=009}}
 +
{{tp|p=32513865|t=2020. Genomic surveillance reveals multiple introductions of SARS-CoV-2 into Northern California.|pdf=|usr=009}}
 +
{{tp|p=32450246|t=2020. Molecular epidemiology of SARS-CoV-2 in Faisalabad, Pakistan: A real-world clinical experience.|pdf=|usr=008}}
 +
{{tp|p=32292587|t=2020. Mutated COVID-19, May Foretells Mankind in a Great Risk in the Future.|pdf=|usr=009}}
 +
{{tp|p=32483490|t=2020. The role of selectivity of the SARS-CoV-2 virus for human genetic profiles in susceptibility and resistance to COVID-19.|pdf=|usr=009}}
 +
{{tp|p=32381617|t=2020. Near-Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Causing a COVID-19 Case in Peru.|pdf=|usr=009}}
 +
{{tp|p=32467284|t=2020. Coding-Complete Genome Sequences of Two SARS-CoV-2 Isolates from Egypt.|pdf=|usr=009}}
 +
{{tp|p=32467283|t=2020. Complete Genome Sequence of SARS-CoV-2 in a Tiger from a U.S. Zoological Collection.|pdf=|usr=009}}
 +
{{tp|p=32409547|t=2020. Complete Genome Sequences of SARS-CoV-2 Strains Detected in Malaysia.|pdf=|usr=009}}
 +
{{tp|p=32527780|t=2020. Complete Genome Sequence of a Novel Coronavirus (SARS-CoV-2) Isolate from Bangladesh.|pdf=|usr=009}}
 +
{{tp|p=32528128|t=2020. Bat-borne virus diversity, spillover and emergence.|pdf=|usr=009}}
 +
{{tp|p=32464496|t=2020. Genetic variation in SARS-CoV-2 may explain variable severity of COVID-19.|pdf=|usr=009}}
 +
{{tp|p=32412415|t=2020. A Snapshot of SARS-CoV-2 Genome Availability up to April 2020 and its Implications: Data Analysis.|pdf=|usr=009}}
 +
{{tp|p=32398273|t=2020. RNA genome conservation and secondary structure in SARS-CoV-2 and SARS-related viruses: a first look.|pdf=|usr=007}}
 +
{{ttp|p=32330414|t=ä. The Architecture of SARS-CoV-2 Transcriptome |pdf=|usr=}}
 
{{tp|p=32289263|t=ä. An Infectious cDNA Clone of SARS-CoV-2 |pdf=|usr=}}
 
{{tp|p=32289263|t=ä. An Infectious cDNA Clone of SARS-CoV-2 |pdf=|usr=}}
 +
*[https://www.sciencedirect.com/science/article/pii/S1567134820301829 genomic var. is high]
 +
{{ttp|p=32341946|t=2020. Chaos game representation dataset of SARS-CoV-2 genome |pdf=|usr=}}
 +
{{tp|p=C7200767|t=2020. Chaos game representation dataset of SARS-CoV-2 genome |pdf=|usr=}}
 +
{{tp|p=32301390|t=2020. Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction |pdf=|usr=}}
 +
{{tp|p=32167166|t=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) |pdf=|usr=}}
 +
{{tp|p=32145215|t=ä. Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2 |pdf=|usr=}}
 +
{{tp|p=32471829|t=2020. Novel Immunoglobulin Domain Proteins Provide Insights into Evolution and Pathogenesis of SARS-CoV-2-Related Viruses.|pdf=|usr=007}}
 +
{{tp|p=32437232|t=2020. Virus-induced genetics revealed by multidimensional precision medicine transcriptional workflow applicable to COVID-19.|pdf=|usr=007}}
 +
{{tp|p=32422894|t=2020. A Novel Synonymous Mutation of SARS-CoV-2: Is This Possible to Affect Their Antigenicity and Immunogenicity?|pdf=|usr=007}}
 +
{{ttp|p=32484220|t=2020. Discovery of G-quadruplex-forming sequences in SARS-CoV-2.|pdf=|usr=007}}
 +
{{tp|p=32472763|t=2020. Comparative analysis of Coronaviridae nucleocapsid and surface glycoprotein sequences.|pdf=|usr=007}}
 +
{{tp|p=32474553|t=2020. Analysis of RNA sequences of 3636 SARS-CoV-2 collected from 55 countries reveals selective sweep of one virus type.|pdf=|usr=007}}
 +
{{tp|p=32492196|t=2020. High-Coverage SARS-CoV-2 Genome Sequences Acquired by Target Capture Sequencing.|pdf=|usr=007}}
 +
{{tp|p=32492183|t=2020. Evidence for mutations in SARS-CoV-2 Italian isolates potentially affecting virus transmission.|pdf=|usr=007}}
 +
{{ttp|p=32420944|t=2020. The impact of MicroRNAs (miRNAs) on the genotype of coronaviruses.|pdf=|usr=007}}
 +
{{ttp|p=32425659|t=2020. Investigating the genomic landscape of novel coronavirus (2019-nCoV) to identify non-synonymous mutations for use in diagnosis and drug design.|pdf=|usr=008}}
 +
{{ttp|p=32522874|t=2020. Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses.|pdf=|usr=008}}
 +
{{tp|p=32416074|t=2020. A Novel Bat Coronavirus Closely Related to SARS-CoV-2 Contains Natural Insertions at the S1/S2 Cleavage Site of the Spike Protein.|pdf=|usr=008}}
 +
{{tp|p=32525765|t=2020. Genetic cluster analysis of SARS-CoV-2 and the identification of those responsible for the major outbreaks in various countries.|pdf=|usr=008}}
 +
{{tp|p=32524946|t=2020. Genetic structure of SARS-CoV-2 reflects clonal superspreading and multiple independent introduction events, North-Rhine Westphalia, Germany, February and March 2020.|pdf=|usr=008}}
 +
{{ttp|p=32473977|t=2020. Unfolding SARS-CoV-2 viral genome to understand its gene expression regulation.|pdf=|usr=008}}
 +
{{tp|p=32501423|t=2020. Developing an ultra-efficient microsatellite discoverer to find structural differences between SARS-CoV-1 and Covid-19.|pdf=|usr=008}}
  
'''genomic variablity'''
+
===structure===
*[https://www.sciencedirect.com/science/article/pii/S1567134820301829 ...is high]
+
{{tp|p=32092911|t=2020. Rigidity of the Outer Shell Predicted by a Protein Intrinsic Disorder Model Sheds Light on the COVID-19 (Wuhan-2019-nCoV) Infectivity |pdf=|usr=}}
 +
{{ttp|p=32362648|t=2020. Transmission electron microscopy imaging of SARS-CoV-2 |pdf=|usr=}}
 +
{{tp|p=32292212|t=2020. Photopolarimetrical properties of coronavirus model particles: Spike proteins number influence |pdf=|usr=}}
 +
{{tp|p=32470119|t=2020. Coronavirus3D: 3D structural visualization of COVID-19 genomic divergence.|pdf=|usr=007}}
 +
{{ttp|p=32493627|t=2020. Structural Proteins in Severe Acute Respiratory Syndrome Coronavirus-2.|pdf=|usr=008}}
 +
{{ttp|p=32446936|t=2020. Electron Microscopic Investigations in COVID-19: Not all Crowns Are Coronas.|pdf=|usr=009}}''renal virus-like structures are normal cell constituents''
 +
{{tp|p=32442529|t=2020. Electron microscopy of SARS-CoV-2: a challenging task.|pdf=|usr=009}}''img of read viral particles''
 +
{{tp|p=32442527|t=2020. Electron microscopy of SARS-CoV-2: a challenging task - Authors' reply.|pdf=|usr=009}}
 +
{{tp|p=32455617|t=2020. Novel Dynamic Structures of 2019-nCoV with Nonlocal Operator via Powerful Computational Technique.|pdf=|usr=007}}
 +
{{tp|p=32470223|t=2020. COVID-19: Structural Predictions of Viral Success.|pdf=|usr=007}}
  
'''nucleocapsid protein'''
 
{{tp|p=32363136|t=ä. Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites |pdf=|usr=}}
 
  
'''spike protein'''
+
===all the proteins===
{{tp|p=32057769|t=2020. The spike glycoprotein of the new coronavirus 2019-nCoV contains a furin-like cleavage site absent in CoV of the same clade |pdf=|usr=}}
+
{{ttp|p=32447571|t=2020. The Proteins of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS CoV-2 or n-COV19), the Cause of COVID-19.|pdf=|usr=009}}
{{tp|p=32155444|t=ä. Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein |pdf=|usr=}}
+
{{tp|p=32462744|t=2020. Shortlisting SARS-CoV-2 Peptides for Targeted Studies from Experimental Data-Dependent Acquisition Tandem Mass Spectrometry Data.|pdf=|usr=009}}
 +
{{tp|p=32083638|t=2020. Processing of the SARS-CoV pp1a/ab nsp7-10 region.|pdf=|usr=011}}
 +
{{tp|p=32596311|t=2020. Sars-CoV-2 Envelope and Membrane Proteins: Structural Differences Linked to Virus Characteristics?|pdf=|usr=011}}
 +
{{tp|p=32604797|t=2020. Data and Text Mining Help Identify Key Proteins Involved in the Molecular Mechanisms Shared by SARS-CoV-2 and HIV-1.|pdf=|usr=011}}
  
'''3CL proteinase'''
+
===primase complex===
{{tp|p=32293875|t=ä. Why Are Lopinavir and Ritonavir Effective against the Newly Emerged Coronavirus 2019? Atomistic Insights into the Inhibitory Mechanisms |pdf=|usr=}}
+
{{ttp|p=32535228|t=2020. Structural analysis of the putative SARS-CoV-2 primase complex.|pdf=|usr=009}}
{{tp|p=32239142|t=ä. Potential covalent drugs targeting the main protease of the SARS-CoV-2 coronavirus |pdf=|usr=}}
+
{{tp|p=32308266|t=2020. Molecular docking and dynamics simulation of FDA approved drugs with the main protease from 2019 novel coronavirus |pdf=|usr=}}
+
{{tp|p=32313296|t=2020. Identification of potential binders of the main protease 3CLpro of the COVID-19 via structure-based ligand design and molecular modeling |pdf=|usr=}}
+
  
'''nsp1 protein'''
+
===nsp===
 +
{{ttp|p=32270884|t=2020. Role of Nonstructural Proteins in the Pathogenesis of SARS-CoV-2 |pdf=|usr=}}
 +
{{tp|p=32275073|t=2020. Response to Ribeiro da Silva et al ,"Role of Nonstructural Proteins in the Pathogenesis of SARS-CoV-2 |pdf=|usr=}}
 +
 
 +
===nsp1 protein===
 
{{tp|p=32336957|t=2020. Combination of Biodata Mining and Computational Modelling in Identification and Characterization of ORF1ab Polyprotein of SARS-CoV-2 Isolated from Oronasopharynx of an Iranian Patient |pdf=|usr=}}
 
{{tp|p=32336957|t=2020. Combination of Biodata Mining and Computational Modelling in Identification and Characterization of ORF1ab Polyprotein of SARS-CoV-2 Isolated from Oronasopharynx of an Iranian Patient |pdf=|usr=}}
----
 
  
{{tp|p=32311462|t=2020. On the molecular determinants of the SARS-CoV-2 attack |pdf=|usr=}}
+
===nsp2 protein===
{{tp|p=32129843|t=ä. Genomic diversity of SARS-CoV-2 in Coronavirus Disease 2019 patients |pdf=|usr=}}
+
{{tp|p=32083328|t=ä. COVID?2019: The role of the nsp2 and nsp3 in its pathogenesis |pdf=|usr=}}
{{tp|p=32129842|t=ä. A glimpse into the origins of genetic diversity in SARS-CoV-2 |pdf=|usr=}}
+
{{tp|p=32229288|t=ä. Molecular characterization of SARS-CoV-2 from the first case of COVID-19 in Italy |pdf=|usr=}}
+
{{tp|p=32341946|t=2020. Chaos game representation dataset of SARS-CoV-2 genome |pdf=|usr=}}
+
{{tp|p=32301390|t=2020. Attenuated SARS-CoV-2 variants with deletions at the S1/S2 junction |pdf=|usr=}}
+
{{tp|p=32178593|t=2020. Emerging WuHan (COVID-19) coronavirus: glycan shield and structure prediction of  spike glycoprotein and its interaction with human CD26 |pdf=|usr=}}
+
{{tp|p=31987001|t=2020. Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated  from a patient with atypical pneumonia after visiting Wuhan |pdf=|usr=}}
+
  
{{tp|p=32265007|t=2020. Whole genome and phylogenetic analysis of two SARS-CoV-2 strains isolated in Italy in January and February 2020: additional clues on multiple introductions and further circulation in Europe |pdf=|usr=}}
+
===nsp3 protein===
{{tp|p=32210741|t=2020. Unrevealing sequence and structural features of novel coronavirus using in silico approaches: The main protease as molecular target |pdf=|usr=}}
+
{{tp|p=32083328|t=ä. COVID?2019: The role of the nsp2 and nsp3 in its pathogenesis |pdf=|usr=}}
{{tp|p=32194944|t=2020. Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL pro) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates |pdf=|usr=}}
+
{{tp|p=29128390|t=2018. Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein |pdf=|usr=}}
{{tp|p=32300673|t=2020. Genomic characterization of a novel SARS-CoV-2 |pdf=|usr=}}
+
{{tp|p=32578982|t=2020. Molecular Basis for ADP-ribose Binding to the Mac1 Domain of SARS-CoV-2 Nsp3.|pdf=|usr=010}}
{{tp|p=32353474|t=ä. Genotyping coronavirus SARS-CoV-2: Methods and implications |pdf=|usr=}}
+
{{ttp|p=32549200|t=2020. A Putative Role of de-Mono-ADP-Ribosylation of STAT1 by the SARS-CoV-2 Nsp3 Protein in the Cytokine Storm Syndrome of COVID-19.|pdf=|usr=011}}
{{tp|p=32362650|t=2020. Genomic analysis of SARS-CoV-2 strains among Indians returning from Italy, Iran & China, & Italian tourists in India |pdf=|usr=}}
+
{{tp|p=32563187|t=2020. Attenuated interferon and pro-inflammatory response in SARS-CoV-2-infected human dendritic cells is associated with viral antagonism of STAT1 phosphorylation.|pdf=|usr=011}}
{{tp|p=32362648|t=2020. Transmission electron microscopy imaging of SARS-CoV-2 |pdf=|usr=}}
+
{{tp|p=32242873|t=2020. Full-genome sequences of the first two SARS-CoV-2 viruses from India |pdf=|usr=}}
+
  
{{tp|p=32092483|t=2020. Genetic diversity and evolution of SARS-CoV-2 |pdf=|usr=}}
+
===nsp6 protein===
{{tp|p=32335334|t=ä. Emerging genetic diversity among clinical isolates of SARS-CoV-2: Lessons for today |pdf=|usr=}}
+
{{tp|p=32283146|t=2020. Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy.|pdf=|usr=008}}
  
{{tp|p=32004758|t=2020. Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event |pdf=|usr=}}
+
===nsp7b===
 +
{{tp|p=32142938|t=2020. Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated  with evolution of 2019-nCoV |pdf=|usr=}}
  
{{tp|p=32361692|t=2020. How the COVID-19 Overcomes the Battle? An Approach to Virus Structure |pdf=|usr=}}
+
===nsp8===
{{tp|p=32306836|t=2020. Novel 2019 coronavirus structure, mechanism of action, antiviral drug promises and rule out against its treatment |pdf=|usr=}}
+
{{tp|p=32142938|t=2020. Nonstructural proteins NS7b and NS8 are likely to be phylogenetically associated  with evolution of 2019-nCoV |pdf=|usr=}}
{{tp|p=32145215|t=ä. Identification of the hyper-variable genomic hotspot for the novel coronavirus SARS-CoV-2 |pdf=|usr=}}
+
{{tp|p=31994738|t=2020. The 2019?new coronavirus epidemic: Evidence for virus evolution |pdf=|usr=}}
+
{{tp|p=32027036|t=2020. Genomic variance of the 2019?nCoV coronavirus |pdf=|usr=}}
+
{{tp|p=32265180|t=ä. Genotype and phenotype of COVID-19: Their roles in pathogenesis |pdf=|usr=}}
+
{{tp|p=32178970|t=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 |pdf=|usr=}}
+
  
{{tp|p=32320687|t=ä. Phylogenetic Analysis and Structural Modeling of SARS-CoV-2 Spike Protein Reveals an Evolutionary Distinct and Proteolytically Sensitive Activation Loop |pdf=|usr=}}
+
===nsp9===
{{tp|p=32200634|t=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 |pdf=|usr=}}
+
{{tp|p=32592996|t=2020. Crystal Structure of the SARS-CoV-2 Non-structural Protein 9, Nsp9.|pdf=|usr=011}}
 +
 
 +
===nsp13 protein NTPase, RNA helicase===
 +
{{tp|p=32500504|t=2020. SARS-Coronavirus-2 Nsp13 Possesses NTPase and RNA Helicase Activities That Can Be Inhibited by Bismuth Salts.|pdf=|usr=009}}
 +
 
 +
===nsp15 endoribonuclease NendoU===
 +
{{tp|p=32304108|t=2020. Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2 |pdf=|usr=}}
 +
 
 +
===papain-like proteinase 2===
 +
{{tp|p=32216114|t=ä. Structural and biochemical characterization of SARS-CoV papain-like protease 2 |pdf=|usr=}}
 +
 
 +
===replication factors===
 
{{tp|p=32321524|t=2020. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant |pdf=|usr=}}
 
{{tp|p=32321524|t=2020. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant |pdf=|usr=}}
{{tp|p=32357959|t=2020. An 81 nucleotide deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020) |pdf=|usr=}}
+
{{tp|p=32277040|t=2020. Structure of the RNA-dependent RNA polymerase from COVID-19 virus |pdf=|usr=}}
 +
{{tp|p=32167173|t=ä. The potential chemical structure of anti?SARS?CoV?2 RNA?dependent RNA polymerase |pdf=|usr=}}
 +
{{ttp|p=32511245|t=2020. A unifying structural and functional model of the coronavirus replication organelle: Tracking down RNA synthesis.|pdf=|usr=007}}
 +
{{tp|p=32438371|t=2020. Structure of replicating SARS-CoV-2 polymerase.|pdf=|usr=007}}
 +
{{tp|p=32443810|t=2020. A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping.|pdf=|usr=007}}
 +
{{tp|p=32427393|t=2020. Telomeres and COVID-19.|pdf=|usr=007}}
 +
{{tp|p=32392072|t=2020. Novel Coronavirus Polymerase and Nucleotidyl-Transferase Structures: Potential to Target New Outbreaks.|pdf=|usr=008}}
 +
{{tp|p=32526208|t=2020. Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase.|pdf=|usr=008}}
 +
{{tp|p=32531208|t=2020. Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2.|pdf=|usr=008}}
  
{{tp|p=32350227|t=2020. Characteristics of SARS-CoV-2 isolated from asymptomatic carrier in Tokyo |pdf=|usr=}}
+
 
{{tp|p=32007145|t=2020. Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding |pdf=|usr=}}
+
===nucleocapsid===
{{tp|p=32342926|t=2020. Properties of Coronavirus and SARS-CoV-2 |pdf=|usr=}}
+
{{tp|p=32363136|t=ä. Crystal structure of SARS-CoV-2 nucleocapsid protein RNA binding domain reveals potential unique drug targeting sites |pdf=|usr=}}
{{tp|p=32194253|t=ä. Molecular basis of COVID-19 relationships in different species: a one health perspective |pdf=|usr=}}
+
 
{{tp|p=32302675|t=ä. Comparative computational analysis of SARS-CoV-2 nucleocapsid protein epitopes in taxonomically related coronaviruses |pdf=|usr=}}
 
{{tp|p=32302675|t=ä. Comparative computational analysis of SARS-CoV-2 nucleocapsid protein epitopes in taxonomically related coronaviruses |pdf=|usr=}}
{{tp|p=32165386|t=2020. Complete Genome Sequence of a 2019 Novel Coronavirus (SARS-CoV-2) Strain Isolated in Nepal |pdf=|usr=}}
+
{{tp|p=32416961|t=2020. Biochemical characterization of SARS-CoV-2 nucleocapsid protein |pdf=|usr=}}
{{ttp|p=32289821|t=ä. Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense |pdf=|usr=}}
+
{{ttp|p=32291557|t=ä. SARS-CoV-2-encoded nucleocapsid protein acts as a viral suppressor of RNA interference in cells |pdf=|usr=}}
 +
{{ttp|p=32562316|t=2020. A proposed role for the SARS-CoV-2 nucleocapsid protein in the formation and regulation of biomolecular condensates.|pdf=|usr=010}}
 +
{{ttp|p=32589897|t=2020. The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway.|pdf=|usr=011}}
 +
 
 +
 
 +
 
 +
===vacuolar interaction===
 +
{{ttp|p=32485205|t=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.|pdf=|usr=008}}
 +
 
 +
 
 +
'''innate interference'''
 +
 
 +
'''virus secretion'''
 +
 
 +
'''envelope'''
 +
{{tp|p=32446902|t=2020. Immunoinformatic analysis of the SARS-CoV-2 envelope protein as a strategy to assess cross-protection against COVID-19.|pdf=|usr=009}}
 +
 
 +
 
 +
===receptor binding any target===
 +
{{ttp|p=32565603|t=2020. Update on the target structures of SARS-CoV-2: A systematic review.|pdf=|usr=011}}
 +
{{tp|p=32604730|t=2020. SARS-CoV-2 Evolutionary Adaptation toward Host Entry and Recognition of Receptor O-Acetyl Sialylation in Virus-Host Interaction.|pdf=|usr=011}}
 +
{{tp|p=32595513|t=2020. New Strategy for COVID-19: An Evolutionary Role for RGD Motif in SARS-CoV-2 and Potential Inhibitors for Virus Infection.|pdf=|usr=011}}
 +
 
 +
*'''[[Target ACE2, Spike protein]]'''
 +
 
 +
===receptor binding: trmpss2===
 +
{{tp|p=32165541|t=2020. Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells |pdf=|usr=}}
 +
{{tp|p=32404436|t=2020. TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes.|pdf=|usr=007}}
 +
{{tp|p=32410502|t=2020. First comprehensive computational analysis of functional consequences of TMPRSS2 SNPs in susceptibility to SARS-CoV-2 among different populations.|pdf=|usr=007}}
 +
{{tp|p=32437018|t=2020. TMPRSS2: Potential Biomarker for COVID-19 Outcomes.|pdf=|usr=007}}
 +
{{tp|p=32468052|t=2020. Pancancer analysis of transmembrane protease serine 2 and cathepsin L that mediate cellular SARSCoV2 infection leading to COVID-19.|pdf=|usr=007}}
 +
 
 +
 
 +
===receptor binding: trmpss4===
 +
{{tp|p=32404436|t=2020. TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes.|pdf=|usr=007}}
 +
 
 +
===receptor binding: grp78, g-proteins===
 +
{{ttp|p=32169481|t=2020. COVID-19 spike-host cell receptor GRP78 binding site prediction |pdf=|usr=}}
 +
{{tp|p=32329083|t=2020. (ang.)COVID-19 transmission through host cell directed network of GPCR |pdf=|usr=}}
 +
 
 +
===candidate receptor binding DPP4===
 +
{{tp|p=32405622|t=2020. The MERS-CoV Receptor DPP4 as a Candidate Binding Target of the SARS-CoV-2 Spike.|pdf=|usr=008}}
 +
 
 +
===Uptake: cathepsin L===
 +
{{tp|p=32468052|t=2020. Pancancer analysis of transmembrane protease serine 2 and cathepsin L that mediate cellular SARSCoV2 infection leading to COVID-19.|pdf=|usr=007}}
 +
 
 +
===endocytosis membrane fusion===
 +
{{tp|p=32047258|t=ä. Fusion mechanism of 2019-nCoV and fusion inhibitors targeting HR1 domain in spike protein |pdf=|usr=}}
 +
{{tp|p=32265513|t=ä. SARS-CoV-2 infects T lymphocytes through its spike protein-mediated membrane fusion |pdf=|usr=}}
 +
{{tp|p=32130973|t=2020. A potential role for integrins in host cell entry by SARS-CoV-2 |pdf=|usr=}}
 +
{{tp|p=32246503|t=ä. SARS?COV?2 and infectivity: Possible increase in infectivity associated to integrin motif expression |pdf=|usr=}}
 +
{{ttp|p=32272173|t=2020. Coronavirus membrane fusion mechanism offers a potential target for antiviral development |pdf=|usr=}}
 +
{{tp|p=32094589|t=ä. Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses |pdf=|usr=}}
 +
{{ttp|p=32376634|t=2020. Cell entry mechanisms of SARS-CoV-2 |pdf=|usr=}}
 +
{{tp|p=32047128|t=2020. Distinct Roles for Sialoside and Protein Receptors in Coronavirus Infection |pdf=|usr=}}
 +
{{ttp|p=32428379|t=2020. Understanding SARS-CoV-2 endocytosis for COVID-19 drug repurposing.|pdf=|usr=007}}
 +
{{tp|p=32479856|t=2020. SARS-CoV-2 entry in host cells-multiple targets for treatment and prevention.|pdf=|usr=008}}
 +
 
 +
 
 +
===3CL proteinase and main proteinase is the same===
 +
{{tp|p=32293875|t=ä. Why Are Lopinavir and Ritonavir Effective against the Newly Emerged Coronavirus 2019? Atomistic Insights into the Inhibitory Mechanisms |pdf=|usr=}}
 +
{{tp|p=32239142|t=ä. Potential covalent drugs targeting the main protease of the SARS-CoV-2 coronavirus |pdf=|usr=}}
 +
{{tp|p=32308266|t=2020. Molecular docking and dynamics simulation of FDA approved drugs with the main protease from 2019 novel coronavirus |pdf=|usr=}}
 +
{{tp|p=32313296|t=2020. Identification of potential binders of the ''main protease 3CLpro'' of the COVID-19 via structure-based ligand design and molecular modeling |pdf=|usr=}}
 +
{{tp|p=32391184|t=2020. Comprehensive Insights into the Catalytic Mechanism of Middle East Respiratory Syndrome 3C-Like Protease and Severe Acute Respiratory Syndrome 3C-Like Protease |pdf=|usr=}}
 +
{{tp|p=32210741|t=2020. Unrevealing sequence and structural features of novel coronavirus using in silico approaches: The main protease as molecular target |pdf=|usr=}}
 +
{{tp|p=32194944|t=2020. Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL pro) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates |pdf=|usr=}}
 +
{{tp|p=32581217|t=2020. Structural plasticity of SARS-CoV-2 3CL M(pro) active site cavity revealed by room temperature X-ray crystallography.|pdf=|usr=010}}
 +
 
 +
 
 +
 
 +
===orf===
 +
{{tp|p=32357959|t=2020. An 81 nucleotide deletion in SARS-CoV-2 ORF7a identified from sentinel surveillance in Arizona (Jan-Mar 2020) |pdf=|usr=}}
 
{{tp|p=32371472|t=2020. SARS-CoV-2 and ORF3a: Nonsynonymous Mutations, Functional Domains, and Viral Pathogenesis |pdf=|usr=}}
 
{{tp|p=32371472|t=2020. SARS-CoV-2 and ORF3a: Nonsynonymous Mutations, Functional Domains, and Viral Pathogenesis |pdf=|usr=}}
{{tp|p=32123347|t=ä. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 |pdf=|usr=}}
+
{{tp|p=32433742|t=2020. Extended ORF8 Gene Region Is Valuable in the Epidemiological Investigation of SARS-similar Coronavirus.|pdf=|usr=007}}
{{tp|p=32303698|t=ä. A map of SARS-CoV-2 and host cell interactions |pdf=|usr=}}
+
{{tp|p=32555321|t=2020. The ORF3a protein of SARS-CoV-2 induces apoptosis in cells.|pdf=|usr=010}}
 +
{{tp|p=32589897|t=2020. The ORF6, ORF8 and nucleocapsid proteins of SARS-CoV-2 inhibit type I interferon signaling pathway.|pdf=|usr=011}}
 +
{{tp|p=32540495|t=2020. Molecular conservation and differential mutation on ORF3a gene in Indian SARS-CoV2 genomes.|pdf=|usr=011}}
 +
{{tp|p=32504060|t=2020. Immune evasion via SARS-CoV-2 ORF8 protein?|pdf=|usr=009}}
  
{{tp|p=32149036|t=2020. Identification of Coronavirus Isolated from a Patient in Korea with COVID-19 |pdf=|usr=}}
 
{{tp|p=32357545|t=2020. Emergence of Drift Variants That May Affect COVID-19 Vaccine Development and Antibody Treatment |pdf=|usr=}}
 
  
{{tp|p=32269081|t=2020. Phylogenetic network analysis of SARS-CoV-2 genomes |pdf=|usr=}}
+
 
{{tp|p=32009228|t=2020. Evolution of the novel coronavirus from the ongoing Wuhan outbreak and modeling of its spike protein for risk of human transmission |pdf=|usr=}}
+
===varia===
{{tp|p=32277040|t=2020. Structure of the RNA-dependent RNA polymerase from COVID-19 virus |pdf=|usr=}}
+
{{ttp|p=32452762|t=2020. SARS-CoV-2 strategically mimics proteolytic activation of human ENaC.|pdf=|usr=007}}
{{tp|p=32075877|t=2020. Cryo-EM structure of the 2019-nCoV spike in the prefusion conformation |pdf=|usr=}}
+
{{tp|p=32200634|t=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 |pdf=|usr=}}
 +
{{ttp|p=32289821|t=ä. Extreme genomic CpG deficiency in SARS-CoV-2 and evasion of host antiviral defense |pdf=|usr=}}
 +
{{tp|p=32123347|t=ä. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 |pdf=|usr=}}
 
{{tp|p=C7152894|t=ä. A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES |pdf=|usr=}}
 
{{tp|p=C7152894|t=ä. A COMPREHENSIVE ANALYSIS OF GENOME COMPOSITION AND CODON USAGE PATTERNS OF EMERGING CORONAVIRUSES |pdf=|usr=}}
{{tp|p=C7085496|t=ä. Structural, glycosylation and antigenic variation between 2019 novel coronavirus  (2019-nCoV) and SARS coronavirus (SARS-CoV) |pdf=|usr=}}
 
{{tp|p=32218151|t=2020. Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins |pdf=|usr=}}
 
{{tp|p=32098422|t=2020. Systematic Comparison of Two Animal-to-Human Transmitted Human Coronaviruses: SARS-CoV-2 and SARS-CoV |pdf=|usr=}}
 
 
{{tp|p=32366025|t=2020. Codon Usage and Phenotypic Divergences of SARS-CoV-2 Genes |pdf=|usr=}}
 
{{tp|p=32366025|t=2020. Codon Usage and Phenotypic Divergences of SARS-CoV-2 Genes |pdf=|usr=}}
{{tp|p=32351056|t=2020. Decoding the evolution and transmissions of the novel pneumonia coronavirus (SARS-CoV-2 / HCoV-19) using whole genomic data |pdf=|usr=}}
 
 
{{tp|p=32348474|t=2020. Expanding our understanding of the role polyprotein conformation plays in the coronavirus life cycle |pdf=|usr=}}
 
 
{{tp|p=32367648|t=2020. SARS-CoV-2 variants: Relevance for symptom granularity, epidemiology, immunity (herd, vaccines), virus origin and containment?|pdf=|usr=}}
 
{{tp|p=32342578|t=2020. The Importance Of Naturally Attenuated Sars-Cov-2 In The Fight Against Covid-19 |pdf=|usr=}}
 
 
{{tp|p=32291894|t=2020. Cytosine drives evolution of SARS-CoV-2 |pdf=|usr=}}
 
{{tp|p=32291894|t=2020. Cytosine drives evolution of SARS-CoV-2 |pdf=|usr=}}
 
{{tp|p=32169673|t=2020. Genetic evolution analysis of 2019 novel coronavirus and coronavirus from other species |pdf=|usr=}}
 
{{tp|p=32349035|t=2020. Genomic Analysis and Comparative Multiple Sequence of SARS-CoV2 |pdf=|usr=}}
 
{{tp|p=32222995|t=ä. Phylogenetic analysis of the first four SARS?CoV?2 cases in Chile |pdf=|usr=}}
 
{{tp|p=32181901|t=ä. A guideline for homology modeling of the proteins from newly discovered betacoronavirus, 2019 novel coronavirus (2019?nCoV) |pdf=|usr=}}
 
{{tp|p=32167180|t=ä. The establishment of reference sequence for SARS?CoV?2 and variation analysis |pdf=|usr=}}
 
{{tp|p=32167166|t=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) |pdf=|usr=}}
 
{{tp|p=32167173|t=ä. The potential chemical structure of anti?SARS?CoV?2 RNA?dependent RNA polymerase |pdf=|usr=}}
 
 
{{tp|p=32159237|t=ä. From SARS and MERS CoVs to SARS?CoV?2: Moving toward more biased codon usage in viral structural and nonstructural genes |pdf=|usr=}}
 
{{tp|p=32159237|t=ä. From SARS and MERS CoVs to SARS?CoV?2: Moving toward more biased codon usage in viral structural and nonstructural genes |pdf=|usr=}}
{{tp|p=32104911|t=ä. Evolutionary history, potential intermediate animal host, and cross?species analyses of SARS?CoV?2 |pdf=|usr=}}
+
{{tp|p=32387562|t=2020. Coding potential and sequence conservation of SARS-CoV-2 and related animal viruses |pdf=|usr=}}
{{tp|p=32083328|t=ä. COVID?2019: The role of the nsp2 and nsp3 in its pathogenesis |pdf=|usr=}}
+
{{tp|p=32294518|t=2020. A comprehensive analysis of genome composition and codon usage patterns of emerging coronaviruses |pdf=|usr=}}
{{ttp|p=32270884|t=2020. Role of Nonstructural Proteins in the Pathogenesis of SARS-CoV-2 |pdf=|usr=}}
+
{{tp|p=32314811|t=2020. Understanding evolution of SARS-CoV-2: a perspective from analysis of genetic diversity of RdRp gene |pdf=|usr=}}
+
{{tp|p=32311094|t=2020. Distinct Viral Clades of SARS-CoV-2: Implications for Modeling of Viral Spread |pdf=|usr=}}
+
{{tp|p=32275073|t=2020. Response to Ribeiro da Silva et al ,"Role of Nonstructural Proteins in the Pathogenesis of SARS-CoV-2 |pdf=|usr=}}
+
 
+
{{tp|p=32238585|t=2020. Isolation and Full-Length Genome Characterization of SARS-CoV-2 from COVID-19 Cases in Northern Italy |pdf=|usr=}}
+
{{tp|p=32238584|t=2020. Computational inference of selection underlying the evolution of the novel coronavirus, SARS-CoV-2 |pdf=|usr=}}
+
{{tp|p=32365353|t=2020. Rapid reconstruction of SARS-CoV-2 using a synthetic genomics platform |pdf=|usr=}}
+
{{tp|p=32216114|t=ä. Structural and biochemical characterization of SADS?CoV papain?like protease 2 |pdf=|usr=}}
+
{{tp|p=32304108|t=2020. Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2 |pdf=|usr=}}
+
{{tp|p=32171191|t=2020.  Genomic analysis of a 2019-novel coronavirus (2019-nCoV) strain in the first COVID-19 patient found in Hangzhou  |pdf=|usr=}}
+

Version vom 14. Juli 2020, 09:05 Uhr

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

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


32336957 2020. Combination of Biodata Mining and Computational Modelling in Identification and Characterization of ORF1ab Polyprotein of SARS-CoV-2 Isolated from Oronasopharynx of an Iranian Patient

nsp2 protein


32083328 ä. COVID?2019: The role of the nsp2 and nsp3 in its pathogenesis

nsp3 protein


32083328 ä. COVID?2019: The role of the nsp2 and nsp3 in its pathogenesis
29128390 2018. Nsp3 of coronaviruses: Structures and functions of a large multi-domain protein
32578982 2020. Molecular Basis for ADP-ribose Binding to the Mac1 Domain of SARS-CoV-2 Nsp3.

32549200 2020. A Putative Role of de-Mono-ADP-Ribosylation of STAT1 by the SARS-CoV-2 Nsp3 Protein in the Cytokine Storm Syndrome of COVID-19.


32563187 2020. Attenuated interferon and pro-inflammatory response in SARS-CoV-2-infected human dendritic cells is associated with viral antagonism of STAT1 phosphorylation.

nsp6 protein


32283146 2020. Evolutionary analysis of SARS-CoV-2: how mutation of Non-Structural Protein 6 (NSP6) could affect viral autophagy.

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.

nsp13 protein NTPase, RNA helicase


32500504 2020. SARS-Coronavirus-2 Nsp13 Possesses NTPase and RNA Helicase Activities That Can Be Inhibited by Bismuth Salts.

nsp15 endoribonuclease NendoU


32304108 2020. Crystal structure of Nsp15 endoribonuclease NendoU from SARS-CoV-2

papain-like proteinase 2


32216114 ä. Structural and biochemical characterization of SARS-CoV papain-like protease 2

replication factors


32321524 2020. Emerging SARS-CoV-2 mutation hot spots include a novel RNA-dependent-RNA polymerase variant
32277040 2020. Structure of the RNA-dependent RNA polymerase from COVID-19 virus
32167173 ä. The potential chemical structure of anti?SARS?CoV?2 RNA?dependent RNA polymerase

32511245 2020. A unifying structural and functional model of the coronavirus replication organelle: Tracking down RNA synthesis.


32438371 2020. Structure of replicating SARS-CoV-2 polymerase.
32443810 2020. A Structural View of SARS-CoV-2 RNA Replication Machinery: RNA Synthesis, Proofreading and Final Capping.
32427393 2020. Telomeres and COVID-19.
32392072 2020. Novel Coronavirus Polymerase and Nucleotidyl-Transferase Structures: Potential to Target New Outbreaks.
32526208 2020. Structural Basis for RNA Replication by the SARS-CoV-2 Polymerase.
32531208 2020. Structural and Biochemical Characterization of the nsp12-nsp7-nsp8 Core Polymerase Complex from SARS-CoV-2.


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


32165541 2020. Enhanced isolation of SARS-CoV-2 by TMPRSS2-expressing cells
32404436 2020. TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes.
32410502 2020. First comprehensive computational analysis of functional consequences of TMPRSS2 SNPs in susceptibility to SARS-CoV-2 among different populations.
32437018 2020. TMPRSS2: Potential Biomarker for COVID-19 Outcomes.
32468052 2020. Pancancer analysis of transmembrane protease serine 2 and cathepsin L that mediate cellular SARSCoV2 infection leading to COVID-19.


receptor binding: trmpss4


32404436 2020. TMPRSS2 and TMPRSS4 promote SARS-CoV-2 infection of human small intestinal enterocytes.

receptor binding: grp78, g-proteins

32169481 2020. COVID-19 spike-host cell receptor GRP78 binding site prediction


32329083 2020. (ang.)COVID-19 transmission through host cell directed network of GPCR

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


32468052 2020. Pancancer analysis of transmembrane protease serine 2 and cathepsin L that mediate cellular SARSCoV2 infection leading to COVID-19.

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


32293875 ä. Why Are Lopinavir and Ritonavir Effective against the Newly Emerged Coronavirus 2019? Atomistic Insights into the Inhibitory Mechanisms
32239142 ä. Potential covalent drugs targeting the main protease of the SARS-CoV-2 coronavirus
32308266 2020. Molecular docking and dynamics simulation of FDA approved drugs with the main protease from 2019 novel coronavirus
32313296 2020. Identification of potential binders of the main protease 3CLpro of the COVID-19 via structure-based ligand design and molecular modeling
32391184 2020. Comprehensive Insights into the Catalytic Mechanism of Middle East Respiratory Syndrome 3C-Like Protease and Severe Acute Respiratory Syndrome 3C-Like Protease
32210741 2020. Unrevealing sequence and structural features of novel coronavirus using in silico approaches: The main protease as molecular target
32194944 2020. Prediction of the SARS-CoV-2 (2019-nCoV) 3C-like protease (3CL pro) structure: virtual screening reveals velpatasvir, ledipasvir, and other drug repurposing candidates
32581217 2020. Structural plasticity of SARS-CoV-2 3CL M(pro) active site cavity revealed by room temperature X-ray crystallography.


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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