2020
DOI: 10.21203/rs.3.rs-25334/v1
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Decoding the structure of RNA-dependent RNA-polymerase (RdRp), understanding the ancestral relationship and dispersion pattern of 2019 Wuhan Coronavirus

Abstract: Most recently, an outbreak of severe pneumonia caused by the infection of 2019-nCoV, a novel coronavirus first identified in Wuhan, China, imposes serious threats to public health. Upon infecting host cells, coronaviruses assemble a multi-subunit RNA-synthesis complex of viral non-structural proteins (nsp) responsible for the replication and transcription of the viral genome. Therefore, the role and inhibition of nsp12 are indispensable. Since there is no crystallographic structure of RdRp is available, so, he… Show more

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Cited by 6 publications
(6 citation statements)
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“…36 These methods are widely used and have been reported to strongly correlate with experimental results. 15,25,[37][38][39][40][41] Each energy term, including vdW, electrostatic, GB, and SA, was calculated as a part of the total binding energy.…”
Section: Binding Energy Difference Estimationsmentioning
confidence: 99%
See 1 more Smart Citation
“…36 These methods are widely used and have been reported to strongly correlate with experimental results. 15,25,[37][38][39][40][41] Each energy term, including vdW, electrostatic, GB, and SA, was calculated as a part of the total binding energy.…”
Section: Binding Energy Difference Estimationsmentioning
confidence: 99%
“…Consequently, researchers have used various methods to reduce risks, including determining the evolutionary pattern between coronaviruses, developing novel vaccines, identifying the mutational landscape, drug repositioning, and developing novel drugs. [10][11][12][13][14][15][16][17] Using multi-omics data to facilitate the control of COVID-19 primarily relies on understanding the SARS-CoV-2 proteome, which comprises sixteen nonstructural proteins (NSP1-NSP16) and four structural proteins S, E, N, and M. 18 These structural proteins have an array of functions, including attachment to the host receptor, transcription, and replication. 19 When attempting to control the spread of SARS-CoV-2, the spike protein and proteases are the main targets for the development of antiviral drugs and vaccines.…”
Section: Introductionmentioning
confidence: 99%
“…To connect the alanine mutations with the binding affinity changes, the binding free energy of each alanine substituted complex was determined. The free energy scoring function (MMGBSA) is an extensively used approach to evaluate the free energy of a protein-ligand, protein-protein and protein-nucleic acids ( Khan et al, 2018 ; Ali et al, 2019 ; Khan et al, 2019 ; Khan et al, 2020a ; Khan et al, 2020b ; Khan et al, 2020c ; Khan et al, 2020d ; Khan et al, 2020e ; Khan et al, 2020f ; Hussain et al, 2020 ). It used the following equation to calculate the free energy.…”
Section: Methodsmentioning
confidence: 99%
“…The data which was collected from Sao Paulo in Brazil is publicly available online to encourage research and implementation of artificial intelligent methods, able to identify an individual infected by COVID-19 through analysis of patient's CT scan. In [11], the authors designed a 3-dimensional structure for 2019-nCoV. To elucidate the 3D structure, a computational modeling approach was applied to give insight into the domain architecture of nsp12.…”
Section: Introductionmentioning
confidence: 99%