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Optimization of the descriptor set was achieved by systematic removal of molecular descriptor groups that were the least significant for the prediction of PAM activity.
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b Bipartite graph that represents the molecular descriptors grouped in each model.
To cope with the large number of structural features (i.e., 4197 local substructures) compared to the number of proteins (2815 for molecular function) in this study, we only used FDR significant descriptor groups to induce rule models.
In the library, 84% of the descriptor groups had a significant overrepresentation of proteins annotated to at least one of the 113 molecular function classes (FDR controlled at 0.05).
A new molecular descriptor based on partial charges is proposed.
Chemical structures were described by the signatures molecular descriptor.
Nowadays, LEL has become a successful molecular descriptor [6].
Descriptors were calculated using Dragon 7.0 software for molecular descriptor calculation [14].
Mordred can calculate an entire molecular descriptor twice as fast as PaDEL-Descriptor.
For small molecular descriptors, we compared our calculated descriptors with those from Dragon, MOE (Molecular Operating Environment from Chemical Computing Group) or MODEL (Molecular Descriptor Lab).
We then constructed a library of commonly reoccurring local descriptors by a) for each local descriptor identifying a group of structurally similar local descriptors and b) selecting a set of 4197 representative, partially overlapping descriptor groups.
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