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The problems with developing a good a contact score are (i) contact definition; (ii) mathematical expressions converting distance differences to scores.
One possible strategy is to estimate the likelihood of having latent TB infection by calculating a contact score that quantifies exposure to and infectiousness of the index case, as was done by Shams et al. [ 16].
A contact score, reflecting the enrichment in contacts between regions of interest as compared to a null model, was computed for early and late replication origins (Fig. 7b and Additional file 8) [ 45].
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Each cohort member was assigned a water contact score for each year preceding infection status assessment.
We documented demographics, clinical characteristics, HIV status, M.tb exposure (using a standard contact score) and M.tb infection status (TST > = 10 mm).
Even when correct constraints are predicted, these may not allow acceptable models given the conformation changes in unbound dockings (e.g. 7cei) or may result in a lower number of acceptable models if a significant number of unacceptable models have a higher surface contact score even when given a correct constraint (e.g 1i4d).
Children were more likely to have a positive TST if they were older (OR 1.2, p < 0.001), had a higher M.tb contact score (OR 1.2, p < 0.001), had received previous TB treatment (OR 4.8, p = 0.06) or previous IPT (OR 3.2, p = 0.01).
Scores comparing intramolecular distances between a model and a structure (contact scores) have different properties than intermolecular distance scores based on optimal superposition.
In our study, a positive TST was associated with increasing age and an increasing M.tb contact score, which is biologically plausible and consistent with other data [ 30, 34].
A second model including M.tb contact score, age, Ascaris IgE and an age interaction term showed that the effect of age was stronger among those children with a positive Ascaris IgE status.
Furthermore, A pocket comparison algorithm, SiteSorter, raised a contact similarity score of 0.14 between the active sites of these two enzymes, indicating that there are similarities between the nature of the contacts each site makes with its co-crystallized ligand [35].
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