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

Hua Cheng; Bong Hyun Kim; Nick V. Grishin

doi:10.1002/prot.21783

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

Hua Cheng, Bong Hyun Kim, Nick V. Grishin

Research output: Contribution to journal › Article › peer-review

17 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 language	English (US)
Pages (from-to)	1162-1166
Number of pages	5
Journal	Proteins: Structure, Function and Genetics
Volume	70
Issue number	4
DOIs	https://doi.org/10.1002/prot.21783
State	Published - Mar 2008

Keywords

Duplication
Homology
Structure alignment

ASJC Scopus subject areas

Structural Biology
Biochemistry
Molecular Biology

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10.1002/prot.21783

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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.",

keywords = "Duplication, Homology, Structure alignment",

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year = "2008",

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AU - Kim, Bong Hyun

AU - Grishin, Nick V.

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AB - 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.

KW - Duplication

KW - Homology

KW - Structure alignment

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

Abstract

Keywords

ASJC Scopus subject areas

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