1997
DOI: 10.1007/pl00006241
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Estimation of evolutionary distances from protein spatial structures

Abstract: Abstract. 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 caus… Show more

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Cited by 45 publications
(36 citation statements)
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“…2C) based on various measures of structural divergence between pairs of three-dimensional models, including PRIDE (31), rmsd_100 (32), the classical root mean square deviation, the Johnson approach (33) and the Grishin procedure (34). Two completely independent measurements of structural divergence (PRIDE and rmsd_100) are shown in the Tables II and III.…”
Section: Resultsmentioning
confidence: 99%
“…2C) based on various measures of structural divergence between pairs of three-dimensional models, including PRIDE (31), rmsd_100 (32), the classical root mean square deviation, the Johnson approach (33) and the Grishin procedure (34). Two completely independent measurements of structural divergence (PRIDE and rmsd_100) are shown in the Tables II and III.…”
Section: Resultsmentioning
confidence: 99%
“…The assumptions are (1) sites evolve independently, (2) x i (t) does not change if no substitutions occur in site i, (3) the probability that a site with a relative rate x remains unchanged after d amino-acid substitutions per site occurred in the protein sequence is e ‫מ‬xd , and (4) the distribution of relative substitution rates among sites does not change with time (Zuckerkandl and Pauling 1965;Tajima and Takezaki 1994;Grishin 1995Grishin , 1997. In our approach we use only these four assumptions, all of which have been explicitly or implicitly made in the previous studies, but each of these studies has included some additional assumptions.…”
Section: Results and Discussion Estimating Evolutionary Distances Usimentioning
confidence: 99%
“…These criteria maximize the likelihood that the sequence similarity reflects homology and that most of the proteins pairs identified using this approach are true orthologs. The fraction of unchanged sites u was estimated from the identity percentage q as u = (q ‫מ‬ q ϱ )/(1 ‫מ‬ q ϱ ), where q ϱ is the expected identity for random sequences Grishin 1997). …”
Section: Comparison Of Protein Sequence Sets From Complete Genomesmentioning
confidence: 99%
“…Assessing the number of substitutions per site, we define the evolutionary distance (Grishin 1997) D between a yeast protein and its orthologous sequences in a reference eukaryote as q = [ln(1 + 2D)]/2D, where q is the fraction of unchanged sites in a sequence alignment of protein pairs (Fraser et al 2002Jordan et al 2003a,b).…”
Section: Evolutionary Distancementioning
confidence: 99%