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Since every node adaptively adjusts its number of neighbors, the parameter k acts as a performance knob to choose a set of backbone nodes and to form a hierarchical topology structure consisting of symmetric links.
MEDELLER thus builds a set of backbone coordinates for the majority of the structure.
It appeared through these experiments that inclusion of a set of backbone probes covering intergenic regions would also contribute to overcome baseline irregularity.
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In this solution initially a backbone network is established which constructed from a set of strong backbone nodes (BBNs) over the ad hoc network.
A local descriptor of protein structure is a set of short backbone fragments centered in three dimensions around a particular amino acid [25], [26].
The dynamics of local structures is captured by comparison of the sampled conformations with a set of representative backbone fragments (Pandini et al., 2010).
That is, we assume that the distance between two adjacent Cα atoms is constant and represent the Cα-trace of a protein using a set of pseudo backbone angles.
After discarding a burn in of 50% we filtered the output trees using PAUP* and a set of "soft" backbone constraints (polytomies representing uncertain parts of the topology), so that all trees were consistent with current knowledge of reptile phylogeny and that subtrees that need to be monophyletic for the calibration points were not violated.
The major difference, however, is that in BD the E⊖, E⊕ and Eø are defined over a bounded infinite and continuous voxel of backbone conformation space; in B RDEE, these terms are defined over a finite set of backbone conformations.
The Q47 chemical shifts also bear a strong resemblance to those of Gln preceding Pro in intrinsically disordered proteins (IDPs), which have a characteristic set of backbone chemical shifts of ∼174 ppm (CO) and ∼53.5 ppm (Cα).
According to Chothia and Lesk (Chothia and Lesk, 1987; Tramontano et al., 1990), five among the six HV loops (L1, L2, L3, H1 and H2) are shown to adopt only a limited set of backbone conformations (named CS) that can be predicted on the basis of the position and nature of specific amino acids in given positions of the antibody sequence.
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