Classifier, supplementary materials
Publication supplementary materials
- Supplementary Table S1 - evaluation results
- Supplementary File S1 - list of used PDB files
- Supplementary File S2 - formulas used for dRMSD score
- Supplementary Figure S1 - Testing set contents
- Supplementary Figure S2 - examples of doublets from merged BPh classes (W_3/4/5BPh)
- Supplementary Figure S3 - Clusters of doublets from merged BPh classes (W_3/4/5BPh and H_7/8/9BPh)
- Supplementary Figure S4 - ClaRNA time benchmarks
O1 - Training set
Download in ZIP file.O2 - Exemplars
Details of evaluation on the testing set
O3 - True-positives:
doublets dectected by ClaRNA and recognized by other classifiers (with the same interaction type)
O4 - False-positives:
doublets dectected by ClaRNA, but not recognized by other classifiers,
or
recognized by other classifiers with different interaction type.
- invalid strand orientation
- WH_cis vs SH_cis
- new base-ribose contacts not detected by FR3D
- contacts consistent with single classifier
- not recognized by other classifiers
- other
O5 - False-negatives: doublets detected by other classifiers, but not recognized by ClaRNA.
Additional materials
- O6 - List of manual changes in the Training Set
- O7 - Dictionary of names used by classifiers
- O8 - Evaluation differences between ClaRNA and other classifiers
(list of cis/trans detection differences on the training/testing set,
list of new base-ribose interactions detected on the training/testing set,
list of different interaction types detections on the training/testing set) - O9 - artificial doublets added to training set (for interaction types not observed in the training set)