Sequence alignment for molecular replacement

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    4 Citations (Scopus)

    Abstract

    This article focuses on the key step of obtaining the best possible sequence alignment of the Query ( the protein you are interested in) to the Target ( a protein of known three-dimensional structure) in order to build a molecular model for molecular replacement. Common sequence-alignment methods are discussed, starting from structural alignment and then moving to pairwise, multiple and profile-profile methods. The limitations of sequence-alignment methods and guidelines on how to judge the likely accuracy of alignment are considered. This is not a detailed tutorial on how to use specific programs; rather, the reader is directed to current tools and techniques that are likely to yield good results.

    Original languageEnglish
    Pages (from-to)25-32
    Number of pages8
    JournalActa Crystallographica Section D: Biological Crystallography
    Volume64
    DOIs
    Publication statusPublished - Jan 2008

    Keywords

    • SECONDARY STRUCTURE PREDICTION
    • PROTEIN SEQUENCES
    • CONFIDENCE LEVELS
    • ACCURACY
    • DATABASE
    • ANNOTATION
    • PROFILES
    • FAMILIES
    • HOMOLOGY

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