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Hence, we created negative datasets synthetically based on co-localization enrichment of interaction between two proteins.
We think that this strategy of deriving negative datasets is more sophisticated than Jansen et al.'s [34] approach.
Because there is no experimentally verified set of non-interacting pairs, negative datasets are usually generated synthetically.
As a result, we constructed an evaluation system for assessing protein interaction reliability using positive datasets obtained from known protein complex and negative datasets derived based on co-localization characteristics.
These entries were used as the "Negative" datasets.
This idea was tested on the same positive dataset and negative datasets.
If the i-th feature has a high F-score, then this feature effectively discriminates between positive and negative datasets.
Homology reductions within positive and negative datasets were performed with similarity threshold 70% between any two peptide sequences.
Both positive and negative datasets were scattered across all major SCOP classes (SCOP class IDs are from a to g).
MCC is always introduced when the positive and negative datasets are out-of-balance from each other.
For this purpose, we used the second SVM model, due to its consistency on both positive and negative datasets of the native-native interfaces.
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