Sentence examples for protein computing from inspiring English sources

INTREPID uses Jensen Shannon (JS) divergence and phylogenetic tree traversal to estimate the evolutionary conservation for each residue in a protein, computing this score at every node encountered on a path from the root of the tree to the leaf corresponding to the sequence of interest.

An extension of this analysis to all confidently identified proteins (E value <10 4) is shown in Figure 2a, where the average TMHMM score of the intact protein (computed as the average TMHMM score of every residue in the protein sequence) is plotted with respect to the average TMHMM score of the observed matched fragment ions from that precursor.

The relative metastabilities of proteins computed using this approach are shown graphically in Fig. 5a, where it can be seen that the logarithms of activities of the non-predominant proteins drop precipitously.

EnrichNet introduces i) a network-based distance between sets of proteins, computed by means of a random walk with a restart procedure; ii) a statistical framework for assessing the significance of distance between two protein sets.

Using this set of true-positives, we computed the enrichment plot of information flow scores by ranking all proteins and computing the hypergeometric score as a function of the protein rank, which is illustrated in Figure 5.

Then we compute the genetic profile similarities for pairs of proteins by computing Pearson's correlation coefficients between their the genetic interaction profiles.

This notion of vertex-specific rankings is applied in IsoRankN to find dense, clique-like clusters of proteins when computing the global alignment of multiple PPI networks.

Because CAPS can identify interacting regions in two proteins by computing the correlation in the pairwise amino acid variability [ 46], we applied CAPS to every pair of proteins encoded by the 16 genes to examine coevolution between amino acid sites.

Case/control ratios for each protein were computed by averaging log2 ratios across all peptides assigned to the protein.

In order to significantly compare the ability of the methods to match the most similar structure to a given target protein, the averages over only the highest TMscore match for each target protein are computed in Table 6.

LPO in units/mg protein was computed with a molar extinction coefficient of 1.56 × 105 M-.