Definition of general topological equivalence in protein structures. A procedure involving comparison of properties and relationships through simulated annealing and dynamic programming

J Mol Biol. 1990 Mar 20;212(2):403-28. doi: 10.1016/0022-2836(90)90134-8.


A protein is defined as an indexed string of elements at each level in the hierarchy of protein structure: sequence, secondary structure, super-secondary structure, etc. The elements, for example, residues or secondary structure segments such as helices or beta-strands, are associated with a series of properties and can be involved in a number of relationships with other elements. Element-by-element dissimilarity matrices are then computed and used in the alignment procedure based on the sequence alignment algorithm of Needleman & Wunsch, expanded by the simulated annealing technique to take into account relationships as well as properties. The utility of this method for exploring the variability of various aspects of protein structure and for comparing distantly related proteins is demonstrated by multiple alignment of serine proteinases, aspartic proteinase lobes and globins.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Aspartic Acid Endopeptidases
  • Endopeptidases*
  • Globins*
  • Methods
  • Molecular Sequence Data
  • Protein Conformation
  • Sequence Homology, Nucleic Acid
  • Serine Endopeptidases*


  • Globins
  • Endopeptidases
  • Serine Endopeptidases
  • Aspartic Acid Endopeptidases