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Molecular docking analysis provides two main clusters of solutions that both indicate the high specificity of 7C8 to the main epitope composed by the stretch of residues FHSQ, which are localized centrally on the V3 region of gp125.
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The most representative cluster of solutions, site M, was observed in more than 75% of the solutions from the TOP10 list (see Methods).
We represented the cluster of solutions by a localization density, defined as the probability of observing a particular subunit at a specific point in space in the cluster of solutions.
A new section entitled 'Selection of the cluster of solutions' has been added to the Materials and methods section.
The domain domain interaction map displays the frequency of contacts between every pair of domains for a given cluster of solutions.
The sequence-specific contacts of residue R74 seen in the lowest energy-structure are not conserved in the cluster of solutions.
We represented the cluster of solutions by individual localization densities, defined as the probability of observing a specific eIF3 domain at a given point in space.
Moreover, the clustering of solutions provided by the traces offers to the biologist a better information on the characteristics of the blocks of elements of the permutation which are being affected by the reversals.
The clustering of solutions and the use of environment restraints (NCS, water) allows to generate dimer conformations exhibiting precision and accuracy similar to the ones observed for the ssNMR structure of the Crh dimer.
Finally, we performed the following analysis: For a given cluster of solutions, we computed the probability of finding a given protein at any point in space (i.e., the localization density map).
After clustering and cross-validation of the final ensemble of solutions (Additional file 1: Figure S11a, Additional file 1: Table S2), we find one cluster of solutions that is in agreement with the cross-validation data, with the lowest energy structure shown in Figure 6a.
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