High-resolution structures of the SARS-CoV-2 2′- O -methyltransferase reveal strategies for structure-based inhibitor design
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Abstract
Crystal structures of an mRNA-capping enzyme from SARS-CoV-2 in complex with its substrates suggest targets for drug design.
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SciScore for 10.1101/2020.08.03.234716: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Structure solution and refinement: The first structure of nsp16/nsp10 from SARS-CoV-2 in complex with SAM with the small unit cell was determined by Molecular Replacement with Phaser (48) from the CCP4 Suite (49) using the crystal structure of the nsp16/nsp10 heterodimer from SARS-CoV as a search model (PDB ID 3R24, (14)). SAMsuggested: (SAM, RRID:SCR_010951)The initial solutions went through several rounds of refinement in REFMAC v. REFMACsuggested: (Refmac, RRID:SCR_014225)5.8.02… SciScore for 10.1101/2020.08.03.234716: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement not detected. Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable not detected. Table 2: Resources
Software and Algorithms Sentences Resources Structure solution and refinement: The first structure of nsp16/nsp10 from SARS-CoV-2 in complex with SAM with the small unit cell was determined by Molecular Replacement with Phaser (48) from the CCP4 Suite (49) using the crystal structure of the nsp16/nsp10 heterodimer from SARS-CoV as a search model (PDB ID 3R24, (14)). SAMsuggested: (SAM, RRID:SCR_010951)The initial solutions went through several rounds of refinement in REFMAC v. REFMACsuggested: (Refmac, RRID:SCR_014225)5.8.0258 (50) and manual model corrections using Coot (51). Cootsuggested: (Coot, RRID:SCR_014222)MolProbity (54) (http://molprobity.biochem.duke.edu/) was used for monitoring the quality of the model during refinement and for the final validation of the structure. MolProbitysuggested: (MolProbity, RRID:SCR_014226)Structural alignment: The PDB coordinates of SARS-CoV nsp16 and nsp10 were analyzed on the FATCAT (29) and PDBFlex servers (55) to perform structural and sequence alignment. FATCATsuggested: (FATCAT, RRID:SCR_014631)Structural alignments and structure figures were downloaded from the servers and modeled in Pymol open source V 2.1 (56). Pymolsuggested: (PyMOL, RRID:SCR_000305)Results from OddPub: Thank you for sharing your data.
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:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- 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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