Sentence examples for docking patterns from inspiring English sources

Multiple consensus MAPK substrate docking patterns have been proposed for eukaryotes, although some exceptions to these patterns do exist [13].

We revise the regular expressions of previously annotated MAPK docking patterns in order to provide a subtype independent motif that annotates all HIV proteins.

In order to further support the feasibility of our new docking patterns as MAPK docking sites, we compared the structures of the HIV matrix protein to those of ERK1/2 substrates.

Domain interactions have also been inferred from protein structure data using information based on geometric association of domain interaction interfaces [17], conserved binding mode analysis from the docking patterns of interacting domains [18], or co-evolutionary analysis [19].

Using sequence alignments of HIV proteins of different subtypes, we show that MAPK docking patterns previously described for human proteins appear on the HIV matrix, Tat, and Vif proteins in a strain dependent manner, but are absent from HIV Rev and appear on all HIV Nef strains.

Other findings around docking patterns are not reported in this article because of space constraints, but they will be reported in a future publication.

Some of the most frequently observed subtypes of HIV proteins MA, Tat, and Vif are missing the docking pattern most often observed in eukaryotic MAPK substrates, whereas Rev does not show the docking pattern on any strains.

The functional significance of this spatial SV docking pattern remains unclear.

Therefore, we searched for the MAPK docking site patterns on HIV sequences gathered from the Los Alamos National Lab LANLL) HIV Sequence Database (http://www.hiv.lanl.gov/), which contains thousands of sequences spanning multiple subtypes and recombinant forms.

We find that only Nef has a consensus MAPK docking site pattern on the most common HIV strains (A1, B, and C).

Enrichment of docking site pattern hits on ERK1/2 substrates was calculated with a one-tailed Fisher's exact test, using phosphorylated dbPTM substrates as a background set.