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URL:
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http://prodata.swmed.edu/malisam
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What you can do:
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Database containing pairs of structural analogs and their alignments.
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Highlights:
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- To find reliable analogs, we developed an approach based on three ideas.
- First, an insertion together with a part of the evolutionary core of one domain family (a hybrid motif) is analogous to a similar motif contained within the core of another domain family.
- Second, a motif at an interface, formed by secondary structural elements (SSEs) contributed by two or more domains or subunits contacting along that interface, is analogous to a similar motif present in the core of a single domain.
- Third, an artificial protein obtained through selection from random peptides or in sequence design experiments not biased by sequences of a particular homologous family, is analogous to a structurally similar natural protein.
- Each analogous pair is superimposed and aligned manually, as well as by several commonly used programs.
- Applications of this database may range from protein evolution studies, e.g. development of remote homology inference tools and discriminators between homologs and analogs, to protein-folding research, since in the absence of evolutionary reasons, similarity between proteins is caused by structural and folding constraints.
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Keywords:
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- Amino Acid Motifs
- protein databases
- molecular models
- sequence alignment
- protein sequence analysis
- protein motif
- motif
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Literature and Tutorials:
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PubMed Link: MALISAM: a database of structurally analogous motifs in proteins
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This record last updated: 05-01-2008
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