Sentence examples for between proteins we calculated from inspiring English sources
To facilitate comparisons between proteins, we calculated the mean pairwise amino acid diversity for each period, defined as the mean number of amino acid differences per site (in other words, the Hamming distance divided by the sequence length).
To test whether functional similarity between duplicate genes was reflected in the network distances between their proteins, we calculated network distance between proteins of each pair of duplicate genes in the S. cerevisiae network.
To measure the similarity between the GO annotations of two proteins, we calculated the maximum depth of the common ancestor of all pairs of GO terms assigned to both proteins (see Methods; Additional file 2; Fig. 2).
To facilitate the identification of the most efficient descriptors of anti HIV drugs against the three proteins, we calculated the correlation between chemical descriptors of the anti-HIV compounds and their IC50/percent inhibition.
To examine correlated motions between different segments of the protein, we calculated the correlation matrix of the coordinates belonging to all C α atoms along the trajectory.
For each protein, we calculated Pearson's correlation coefficients between each sequence profile and each structural profile.
To examine the relationship between promoter conservation and protein conservation, we calculated the correlation coefficient of promoter conservation (raw alignment score obtained by water) and protein conservation (percentage identity obtained by water).
To determine correlation between mRNA expression and protein expression, we calculated Spearman's rank correlation coefficient.
Correlations (nonlinear) between proteins were calculated using the Spearman rank test.
Pairwise distances between proteins were calculated in MEGA 4.0 [ 26] with the amino acid Poisson correction model, uniform rates among sites and lineages, pairwise deletion.
For the neighbor joining analysis, pairwise distances between proteins were calculated using the Prodist program, and the tree topology was determined using the Neighbor program, both in the Phylip package (v. 3.6; [ 58]).
