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The enumeration model grows larger super-secondary structure patterns (SSPs) by combining pairs of smaller patterns, a process that approximates a potential path of protein fold evolution.
Bioinformatic analyses can trace the path of protein evolution at the sequence level and match this to the corresponding change in function.
The p300/CoA crystals also contain two poly ethylene glycol) moieties bound proximal to the cofactor binding site, implicating the path of protein substrate association.
The p300/CoA crystals also reveal two PEG moieties bound proximal to the cofactor binding site, thus implicating a path of protein substrate association.
(9) v i c i n i t y s, α = { u | u ∈ V p p i, d i s t a n c e G s i m s, u ≤ α } α was chosen by estimating the diameter (length of longest shortest path) of protein complex cores.
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We note that the path of the protein backbone is not directly resolved this region of our density map, which means that the corresponding EM potential tends to uniformly pull backbone atoms toward the center of the loop feature (where density values are highest), and thus away from their true path.
However, in Figure 4B, two pathways share a complete path of three proteins which does not connect to any other distinct part within each pathway and hence these proteins are unlikely to contribute to an interaction between the pathways.
We found the evolution path of Cide proteins is in good agreement with the hypothesis.
In this way, a cluster may contain proteins that by themselves do not share a sequence identity >30% but that are connected through a path of similar proteins.
Before the deletion of the PPI, the shortest path
Betweenness measures how frequently the shortest path connecting every pair of proteins is going through a given protein [ 26].
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