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We introduced an integrated scoring system that uses a novel combination of a set of five orthogonal scoring features covering the probabilistic, evolutionary, evidence-based, spatial and functional properties of interacting domains, which can map the interacting propensity of two domains in many dimensions.
To map the interacting domains, we generated in-frame One-STrEP and HA-tagged truncation mutants of the key domains of IRF5 and FLAG-tagged truncation mutants of the key domains of RelA.
Rather than pursuing analysis of the complex through further biochemical investigations, we identified and characterized mutations that partially disrupt the complex as a means to determine the functional significance of complete and partial complexes, and also map the interacting domains.
Yeast-two-hybrid tests with MP and BRM revealed that no other plant proteins are required for the physical interaction and allowed us to map the interacting region of MP to its middle domain, which is critical for transcriptional activation (Tiwari et al., 2003).
For data integration we map the interacting proteins from external or database specific identifiers to unique protein identifiers from UniProt and EntrezGene [ 49] to enable the combination of the different data sets to one comprehensive set of interaction data for each species.
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In fact, the idea of mapping the interacting regions (IRs) involved in a PPI has been previously suggested for several large-scale screens [15], [16], [17], [18].
We mapped the interacting domains between VAB-19 and EPS-8 in yeast (Figure 1A) and found that the central domain of EPS-8 (residues 272 502) was necessary for binding VAB-19.
This cell cycle specific TF-TF network was further enriched by manually mapping the interacting miRNAs with data collected from the miReg [ 17], TransmiR [ 31], and CircuitsDB [ 32] databases and from literature mining to create a TF-miRNA-TF interaction map.
(Additional file 2: Figure S2) shows the genotype-phenotype map for the interacting pairs.
The mutations that 'compensate' for the defect should map on the interacting partners of the defective element, in the local network of the affected gene(s).
GST-GRD was then used to map the GAPA interacting part in Filamin.
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