Conformational Ensembles of Noncoding Elements in the SARS-CoV-2 Genome from Molecular Dynamics Simulations
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SciScore for 10.1101/2020.12.11.421784: (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 MD simulations were conducted using the Amber ff99SB force field with parmbsc0 (Pérez et al., 2007), OL3 (Zgarbová et al., 2011), and corrections to the Van der Waals parameters for oxygen (Steinbrecher et al., 2012) in conjunction with OPC water model (Izadi et al., 2014). Ambersuggested: (AMBER, RRID:SCR_016151)Simulations were performed using GROMACS 2019.4 (Pronk et al., 2013) patched with PLUMED 2.5.3 (Tribello et al., 2014). GROMACSsuggested: (GROMACS, RRID:SCR_014565)Results from OddPub: Thank you for sharing your code.
Results from LimitationRecognizer: An explicit section about the …SciScore for 10.1101/2020.12.11.421784: (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 MD simulations were conducted using the Amber ff99SB force field with parmbsc0 (Pérez et al., 2007), OL3 (Zgarbová et al., 2011), and corrections to the Van der Waals parameters for oxygen (Steinbrecher et al., 2012) in conjunction with OPC water model (Izadi et al., 2014). Ambersuggested: (AMBER, RRID:SCR_016151)Simulations were performed using GROMACS 2019.4 (Pronk et al., 2013) patched with PLUMED 2.5.3 (Tribello et al., 2014). GROMACSsuggested: (GROMACS, RRID:SCR_014565)Results from OddPub: Thank you for sharing your code.
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.
- No funding statement was detected.
- No protocol registration statement was detected.
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