Structural genomics and interactomics of 2019 Wuhan novel coronavirus, 2019-nCoV, indicate evolutionary conserved functional regions of viral proteins
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Abstract
During its first month, the recently emerged 2019 Wuhan novel coronavirus (2019-nCoV) has already infected many thousands of people in mainland China and worldwide and took hundreds of lives. However, the swiftly spreading virus also caused an unprecedentedly rapid response from the research community facing the unknown health challenge of potentially enormous proportions. Unfortunately, the experimental research to understand the molecular mechanisms behind the viral infection and to design a vaccine or antivirals is costly and takes months to develop. To expedite the advancement of our knowledge we leverage the data about the related coronaviruses that is readily available in public databases, and integrate these data into a single computational pipeline. As a result, we provide a comprehensive structural genomics and interactomics road-maps of 2019-nCoV and use these information to infer the possible functional differences and similarities with the related SARS coronavirus. All data are made publicly available to the research community at http://korkinlab.org/wuhan
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SciScore for 10.1101/2020.02.10.942136: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Each of 2019-nCoV proteins was then aligned with the found related coronavirus proteins using a multiple sequence alignment method Clustal Omega [71] Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Structural characterization of protein and protein complexes: The structure of each protein has been determined using a single-template comparative modeling protocols with MODELLER software package [72]. MODELLERsuggested: (MODELLER, RRID:SCR_008395)Next, to create an integrated network, the two individual networks were imported in Cytoscape [79] and merged to form a unified interactome … SciScore for 10.1101/2020.02.10.942136: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Each of 2019-nCoV proteins was then aligned with the found related coronavirus proteins using a multiple sequence alignment method Clustal Omega [71] Clustal Omegasuggested: (Clustal Omega, RRID:SCR_001591)Structural characterization of protein and protein complexes: The structure of each protein has been determined using a single-template comparative modeling protocols with MODELLER software package [72]. MODELLERsuggested: (MODELLER, RRID:SCR_008395)Next, to create an integrated network, the two individual networks were imported in Cytoscape [79] and merged to form a unified interactome representing both intra-viral and virus-host interactions. Cytoscapesuggested: (Cytoscape, RRID:SCR_003032)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- No conflict of interest statement was detected. If there are no conflicts, we encourage authors to explicit state so.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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