Estimation of evolutionary distances from protein spatial structures

Research output: Contribution to journalArticlepeer-review

35 Scopus citations


New equations are derived to estimate the number of amino acid substitutions per site between two homologous proteins from the root mean square (RMS) deviation between two spatial structures and from the fraction of identical residues between two sequences. The equations are based on evolutionary models, analyzing predominantly structural changes and not sequence changes. Evolution of spatial structure is treated as a diffusion in an elastic force field. Diffusion accounts for structural changes caused by amino acid substitutions, and elastic force reflects selection, which preserves protein fold. Obtained equations are supported by analysis of protein spatial structures.

Original languageEnglish (US)
Pages (from-to)359-369
Number of pages11
JournalJournal of Molecular Evolution
Issue number4
StatePublished - 1997


  • Evolutionary distance
  • Molecular evolution
  • Protein structure
  • RMS deviation
  • Substitution rates

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics


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