MALISAM -- Manual ALIgnments for Structurally Analogous Motifs

What you can do:
Database containing pairs of structural analogs and their alignments.
  • 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.
  • Amino Acid Motifs
  • protein databases
  • molecular models
  • sequence alignment
  • protein sequence analysis
  • protein motif
  • motif
This record last updated: 05-01-2008
Report a missing or misdirected URL.

The Health Sciences Library System supports the Health Sciences at the University of Pittsburgh.

© 1996 - 2023 Health Sciences Library System, University of Pittsburgh. All rights reserved.