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Systematic study on the interaction spectra of inhibitors with multiple human GPCRs will shed light on how to design the inhibitors for different diseases which are related to GPCRs.
Advanced GBA approaches, such as clustering genes based on correlated interaction spectra across multiple interaction partners (Carter et al. 2009; Collins et al. 2007; Costanzo et al. 2010; Drees et al. 2005; Segre et al. 2005), have successfully mapped genetic architecture on a large scale.
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The protein protein interaction spectrum of WSA206 comprises 40% of those MADS and non-MADS-box proteins implicated in floral/anther expression and embryogenesis.
In this paper, we present a method called SimBoost that predicts continuous (non-binary) values of binding affinities of compounds and proteins and thus incorporates the whole interaction spectrum from true negative to true positive interactions.
As pointed out in [4], drawbacks of the binary problem formulation are that true-negative interactions and untested drug target pairs are not differentiated, and that the whole interaction spectrum, including both true-positive and true-negative interactions, is not covered well.
Mutualistic and parasitic networks are on opposite ends of the interaction spectrum in terms of the relationship of the participants (from +/+ to +/−), and nonetheless they appear to share a similar network structure.
Of note, vatalanib was generally well tolerated, which is in line with its narrow kinase interaction spectrum.
Vatalanib is active despite its narrow kinome interaction spectrum in patients diagnosed with imatinib-resistant GIST or with imatinib and sunitinib-resistant GIST.
Overall, our network analysis, supported by the example of TAF1, suggests that common features underlie the genetic interaction spectrum of mutants with genome instability.
The broad interaction spectrum of a hub protein has intrigued researchers to perform in-depth investigation on some exemplary hub proteins like the calmodulin family proteins (42), the WD domain-containing proteins (43) and the coiled-coil proteins (44).
For instance, on the basis of the same reference set of known interactions on a common set of shared mutant pairs in the SGA and GIM datasets, the GIM approach seems to detect particularly well larger number of negative interactions (Table 4), whereas the nearly genome-wide SGA dataset provides comparable detection power in the positive end of the genetic interaction spectrum.
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