Llamanade: An open-source computational pipeline for robust nanobody humanization

  1. Zhe Sang
  2. Yufei Xiang
  3. Ivet Bahar
  4. Yi Shi

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Abstract

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  1. Version published to 10.1016/j.str.2021.11.006
  2. ScreenIT

    SciScore for 10.1101/2021.08.03.455003: (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

    Antibodies
    SentencesResources
    Anti-T7 tag HRP-conjugated secondary antibodies were diluted at 1:5000 and incubated at room temperature for 1 hour.
    Anti-T7 tag
    suggested: None
    Software and Algorithms
    SentencesResources
    To obtain the T20 score of a given VH/VHH sequence, the query sequence will be searched against the reference database by blastp.
    blastp
    suggested: (BLASTP, RRID:SCR_001010)
    Structural analysis of buried residues: The degree of burial for a residue is quantified by measuring the depth of the side chain below the protein surface using the ResidueDepth module in BioPython.
    BioPython
    suggested: (Biopython, RRID:SCR_007173)
    The following criteria were used to predict the presence of a certain interaction: Salt bridge: The distance between two opposite charge atoms between two residues is less than 4 angstrom.
    Salt
    suggested: (SALT, RRID:SCR_003187)
    The raw data were processed and fitted into the 4PL curve using the Prism Graphpad 9.0.
    Graphpad
    suggested: (GraphPad, RRID:SCR_000306)

    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:
    • 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.

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

    About SciScore

    SciScore is an automated tool that is designed to assist expert reviewers by finding and presenting formulaic information scattered throughout a paper in a standard, easy to digest format. SciScore checks for the presence and correctness of RRIDs (research resource identifiers), and for rigor criteria such as sex and investigator blinding. For details on the theoretical underpinning of rigor criteria and the tools shown here, including references cited, please follow this link.

  3. Version published to 10.1101/2021.08.03.455003v1 on bioRxiv