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A number of molecular recognition features have been exploited in structure-based design of selective Cathepsin inhibitors.
The advantage of such a method is that polypeptides can be specifically designed as building blocks incorporated with molecular recognition features and spatially distributed bioactive ligands that would provide a physiological environment for cells in vitro and in vivo.
Generating pharmacophore models which encode accurate molecular recognition features are highly dependent on properly defined annotations.
There are elements, known as molecular recognition features (MoRFs), located within longer IDPRs, that are disordered in their unbound state and fold upon interaction with specific partners (Oldfield et al., 2005), mediating IDP/IDPR binding via disorder-to-order-transition-based recognition involved in many biological processes (Disfani et al., 2012).
For instance, the polyproline-II (PPII) helix is a ubiquitous helical structure motif that is found in extended conformation and is abundant in molecular recognition features (MoRF) of unstructured regions [32].
IDPs that function by molecular recognition, on the other hand, usually bind their partner via short recognition elements termed preformed structural elements, PSEs [53], molecular recognition features, MoRFs [54] or short linear motifs, SLiMs [55].
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This intrinsically disordered segment in the AB loop apparently represents a molecular recognition feature (MoRF), as it undergoes a disorder-to-order transition and becomes structured upon binding to its partner protein, i.e., the C-terminal tail of GG-SpaD.
They are now recognized as a Molecular Recognition Feature (MoRF) [ 38, 45].
The concept of the "molecular recognition feature," abbreviated as MoRF, was introduced to describe short, intrinsically disordered regions that "morph" from disorder-to-order upon partner recognition [ 34- 36].
The predictor of an α-helix forming Molecular Recognition Feature (α-MoRF) is based on observations that predictions of order in otherwise highly disordered proteins corresponds to protein regions that mediate interaction with other proteins or DNA.
In the EFA-6 N-terminus the 18 aa motif is predicted to have relative structural order, and might act as a molecular recognition feature as in other IDPs.
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