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Intuitively, longer insertions or deletions should have more pronounced effects on protein function than shorter ones.
For mutational burden analysis we defined potentially pathogenic variants as not present in dbSNP, conserved and as having deleterious effects on protein function as determined by two out of three bioinformatic functional prediction tools.
Other mutations of the plastid DNA might have occurred, but these resulted either in no exchange of the encoded amino acid or a conservative (functionally similar) amino acid exchange likely without negative effects on protein function.
However, their effects on protein function cannot be readily to predict; thus we focused on genes that were completely deleted.
To discover key contributors, we first identified nonsynonymous single-nucleotide polymorphisms in conserved genomic regions that are predicted to have significant effects on protein function.
Anion effects on protein function typically involve binding to positively charged lysine or arginine residues.
Similar(10)
For membrane-bound enzymes, interference from complex nanoparticle-membrane interactions (due to membrane curvature or vesicle rupture) can skew results and complicate the interpretation of the nanoparticle-induced effects on protein functions unless additional steps are taken to remove it.
The effects on protein functions of non-synonymous SNPs were predicted using the SIFT algorithm [ 27] and Align GVGD [ 28].
According to the SNPEff manual [ 22], this category includes non-coding variants or variants affecting non-coding genes, which are unlikely to have marked effects on protein functions.
Both positive and negative effects on protein functions by sumoylation have been reported (Depaux et al, 2007; Karamouzi et al, 2008).
This may be because longer AAR repeats have such detrimental effects on protein functions that they are apt to be selected out in the genome [ 10, 41, 42].
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