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This reduction in accuracy was largely due to false positives (21 of 159), that is, variants predicted to be functionally disruptive, although no experiment confirms this prediction.
Although these relatively common (1 5% frequency) variants were computationally predicted to be functionally benign (22), our experimental data provide molecular evidence that they could have functional impact in cellular signaling regulation as well.
These residues which were predicted to be functionally relevant were subjected to site-directed mutagenesis and were replaced with alanine.
473 genes were predicted to be functionally linked (via phylogenetic profiling) with genes known to be involved in LAM biosynthesis (Table 2).
The six most highly associated SNPs are either predicted to be functionally significant or are in LD with such a variant.
This signaling mechanism is predicted to be functionally similar to other posttranslation modifications such as phosphorylation, SUMOylation or acetylation, because the added moiety changes the activity of the modified protein.
Similar(23)
A residue with a higher score is thus predicted to be more functionally important than a residue with a lower score.
By analyzing the predicted structures and the conservation of functional motifs, 4 ORFans (R843, L374, R277, L759) were predicted to be enzymes which we functionally characterized as carboxylesterase/thioesterase, metal-dependent deacetylase, P-loop kinase and 3-methyladenine DNA glycosylase, respectively.
4 ORFans (R843, R277, L759 and L374) were predicted to be enzymes and we functionally categorized them as carboxylesterase/thioesterase, P-loop kinase, 3-methyladenine DNA glycosylase and metal-dependent deacetylase, respectively.
SNPs that are located within coding regions and result in a change in the peptide sequence may be classified as 'damaging' or 'altering' if predicted to be in structurally or functionally important sites of the three dimensional structure of the protein.
This analysis resulted in the identification of four protein families that are predicted to be co-expressed and thus functionally linked with the pAgos.
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