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PrePS did correctly predict farnesyltransferase and geranylgeranyltransferase modification sites for human c-K-ras2 protein isoform a.
Nuclear speckles are sites for pre-mRNA splicing that serve as storage and/or modification sites for splicing factors [ 47].
There are a number of bioinformatic software tools available for predicting modification sites for other PTMs [ 64].
A simple algorithm has been devised to incorporate transmembrane domains and protein modification sites for scoring membrane proteins.
However, relative to sequenced genomes/identified snoRNAs, the number of species for which modification sites for rRNA have been experimentally characterized is comparatively low [ 9].
Many computational programs [ 4, 7- 9] have been developed to identify enriched regions (referring to either binding sites or histone modification sites) for the ChIP-seq data.
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As the lysine 164 of PCNA is the modification site for both ubiquitin and SUMO (Bergink and Jentsch, 2009), to investigate whether NEDD8 also targets PCNA at Lys164, we constructed a mutant, PCNA-K164R, and examined its NEDDylation.
The presence of hydroxyl groups at the C4 and C7 positions in coumarin backbone has been proposed as a potential modification site for providing excellent bioactivity according to previous studies.
A regulatory mechanism reported for the Sirt1 C-terminus is to act as a modification site for regulatory phosphorylations [ 18].
In several cases, REases efficiency can depend on the number of restriction-modification sites, for example Ecl18kI, EcoRII, etc. are more active when DNA possesses several restriction sites [ 58, 59].
In NPrEC, we identified 116 protein-SNOs, with modification sites located for 86 of them by the use of a combined protocol involving both protein and peptide pull-down following the BST.
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