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    Nucleic Acids Res. 2007 Jul;35(Web Server issue):W499-502. Epub 2007 May 30.

    FRalanyzer: a tool for functional analysis of fold-recognition sequence-structure alignments.

    Source

    Computer Science and Engineering Department, 201 Bell Hall University at Buffalo, Buffalo, NY 14260, USA. hksaini@cse.buffalo.edu

    Abstract

    We describe FRalanyzer (Fold Recognition alignment analyzer), a new web tool to visually inspect sequence-structure alignments in order to predict functionally important residues in a query sequence of unknown function. This tool is aimed at helping to infer functional relationships between a query sequence and a template structure, and is particularly useful in analyzing fold recognition (FR) results. Because similar folds do not necessarily share the same function, it is not always straightforward to infer a function from an FR result alone. Manual inspection of the FR sequence-structure alignment is often required in order to search for conservation of functionally important residues. FRalanyzer automates parts of this time-consuming process. FRalanyzer takes as input a sequence-structure alignment, automatically searches annotated databases, displays functionally significant residues and highlights the functionally important positions that are identical in the alignment. FRalanyzer can also be used with sequence-structure alignments obtained by other methods, and with structure-structure alignments obtained from structural comparison of newly determined 3D-structures of unknown function. Fralanyzer is available at http://fralanyzer.cse.buffalo.edu/.

    PMID:
    17537819
    [PubMed - indexed for MEDLINE]
    PMCID:
    PMC1933221
    Free PMC Article

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