Table 1 List of Galaxy Tools developed as part of GCAC: The GCAC suite comprises mainly four major tasks. Each task contains one repository and at least one tool associated with it. The GCAC tools are available in galaxy main toolshed (https://toolshed.g2.bx.psu.edu/repository?repository_id=351af44ceb587e54)
From: GCAC: galaxy workflow system for predictive model building for virtual screening
Major Tasks | Toolshed Repositories | Tool Name | Description |
|---|---|---|---|
Descriptor Calculation | padel_descriptor_calculation | PaDELDescriptor | calculates descriptors for active and inactive datasets. |
activity_files_merge | Merge Activity Files | assigns response values and merges positive and negative datasets. | |
redundant_entries_remove | Remove Redundancy | removes redundant entries of molecules. | |
Feature Selection | feature_selection | Feature Selector | selects best features subset |
Model Building and Prediction | csv_to_rdata | Prepare input file | converts csv_files to RData format |
rcaret_classification_model | R-Caret Classification Model-Builder | builds classification model using ‘caret’ R package | |
activity_predict | Predict Activity | predicts activity of molecules using their descriptor file (prediction set) and supplied model. | |
Candidate Compound Extraction | candidate_compound_select | Candidate Compound Selector | selects compound name or ids of interesting molecules based on certain cutoff range. |
compound_id_extract | CompoundID Extractor | extracts compound IDs to be used in downstream compound extraction from sdf files | |
mayatools_extract | ExtractFromSDFiles | provides sdf file of extracted compounds from the prediction set |