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This makes it possible to scan a large number of potentially correct constraints, lowering the requirements for useful contact predictions.
From our results we can conclude that efficient constraint propagation allows us to screen a large number of potentially correct constraints and thus make use of even very noisy data.
The bottom row shows the average gain in acceptable models in each case, given by the total number of acceptable models using constraints divided by the total without constraints (including all complexes, even those without correct constraints).
> -wrap-foot> top top five complexes are those for which no true contact was ranked in the highest ranking 100 predicted contacts and had no correct constraints among the 100 used in docking.
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).
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The top five rows of Table 1 show cases where no correct constraint was identified in the set of 100 constraints used, so in theses cases constrained docking tends to give worse results, although some constraints may be incorrect by a sufficiently small margin to still allow acceptable models and even compensate the difficulties of unbound docking, as happens in complex 1akj.
The epidemiologic design also corrected constraints present in other monitoring systems, such as the temporal and spatial dissociation of human, food, and animal isolates, as well as the lack of uniform laboratory methods.
This step insures the quality of the data, but is also necessary to apply correct physical constraints (2) in the reconciliation method.
The initial stoichiometric matrix was generated based on KEGG and ScoCyc and manually curated to refine the S. coelicolor-specific parts of the metabolic network (e.g., antibiotic biosynthesis), to specify the correct reversibility constraints of reactions, and to add missing essential reactions.
Table 1 Performance comparison of our affine-constraint method with angular-constrained and unconstrained tracking methods Affine Angular No constraint constraint constraint Correct 114 104 103 Lost 6 16 17 .
We thus used the 50% rate to correct the constraint estimates we computed for PITA sites, and we estimate that constraint on the top 15000 PITA sites is 7 8.5% higher than recorded in Table S3.
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