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

Hua Cheng, Bong Hyun Kim, Nick V. Grishin

Research output: Contribution to journalArticle

15 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)1162-1166
Number of pages5
JournalProteins: Structure, Function and Genetics
Volume70
Issue number4
DOIs
StatePublished - Mar 1 2008

Keywords

  • Duplication
  • Homology
  • Structure alignment

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology

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