MALIDUP: A database of manually constructed structure alignments for duplicated domain pairs

Authors

  • Hua Cheng,

    1. Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
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  • Bong-Hyun Kim,

    1. Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
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  • Nick V. Grishin

    Corresponding author
    1. Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
    2. Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9050
    • HHMI/Biochemistry, University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390-9050
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Abstract

We describe MALIDUP (manual alignments of duplicated domains), a database of 241 pairwise structure alignments for homologous domains originated by internal duplication within the same polypeptide chain. Since duplicated domains within a protein frequently diverge in function and thus in sequence, this would be the first database of structurally similar homologs that is not strongly biased by sequence or functional similarity. Our manual alignments in most cases agree with the automatic structural alignments generated by several commonly used programs. This carefully constructed database could be used in studies on protein evolution and as a reference for testing structure alignment programs. The database is available at http://prodata.swmed.edu/malidup. Proteins 2008. © 2007 Wiley-Liss, Inc.

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