Sequence-assignment validation in cryo-EM models with checkMySequence

  1. Grzegorz Chojnowski

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Abstract

The availability of new artificial intelligence-based protein-structure-prediction tools has radically changed the way that cryo-EM maps are interpreted, but it has not eliminated the challenges of map interpretation faced by a microscopist. Models will continue to be locally rebuilt and refined using interactive tools. This inevitably results in occasional errors, among which register shifts remain one of the most difficult to identify and correct. Here, checkMySequence , a fast, fully automated and parameter-free method for detecting register shifts in protein models built into cryo-EM maps, is introduced. It is shown that the method can assist model building in cases where poorer map resolution hinders visual interpretation. It is also shown that checkMySequence could have helped to avoid a widely discussed sequence-register error in a model of SARS-CoV-2 RNA-dependent RNA polymerase that was originally detected thanks to a visual residue-by-residue inspection by members of the structural biology community. The software is freely available at https://gitlab.com/gchojnowski/checkmysequence.

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  1. Version published to 10.1107/s2059798322005009
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    SciScore for 10.1101/2022.01.04.474974: (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
    SentencesResources
    For each of the half-map pairs local resolution maps were calculated using Resmap version 1.1.4 (Kucukelbir et al., 2014) with default parameters.
    Resmap
    suggested: None
    It was developed in Python 3 with an extensive use of pytorch (Paszke et al., 2019), numpy (Oliphant, 2006), scipy (Virtanen et al., 2020), CCTBX (Grosse-Kunstleve et al., 2002) and CCP4 (Winn et al., 2011) libraries and utility programs.
    Python
    suggested: (IPython, RRID:SCR_001658)
    scipy
    suggested: (SciPy, RRID:SCR_008058)
    For making sequence database queries we use HMMER suite version 3.3.2.
    HMMER
    suggested: (Hmmer, RRID:SCR_005305)

    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.
    • Thank you for including a protocol registration statement.

    Results from scite Reference Check: We found no unreliable references.

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  3. Version published to 10.1101/2022.01.04.474974v1 on bioRxiv