Supporting Information for SILCS-xTAC method paper, Nordquist et al.
- protac-loocv.py: python script to perform LOO-CV/RFE fitting and produce figures to describe fitting
- pair_list_dc50.txt : file describing list of data to loop over (enables looping over a subset as desired)
- protac_data.csv: csv file containing SILCS-PROTAC metrics and experimental DC50 data; NOTE: only assays with > 3 entries were considered in final analyses, and there are "duplicate" PROTACS which appear in multiple different, but related, assays
- protac_data.pkl: python pkl file containing SILCS-PROTAC metrics and experimental DC50 data
- environment.yml: conda environment yml file to replicate the python packages used by silcs-protac
- loocv_rfe_results: csv of LOO-CV/RFE results
- figs: contains LOO-CV/RFE figures and general models aggregated for each number of SILCS-PROTAC metric subsets
- random-trial: results from 10 replicas of LOO-CV/RFE fitting on randomized data
- sdf_smiles: contains smiles.csv and directories for each system containing sdf and svg (image) files of PROTACs and warheads
- smiles.csv: csv file with smiles strings of each PROTAC and warheads
- mcs_highlight_warheads.py: draws svg image of PROTACs with warheads highlighted
- draw_grid.py: helper script to assemble svg images into a grid
- create_sdf_smiles_csv.py: helper script to make smiles.csv
- Each system directory contains the sdf format files and a grid-style svg image of the protacs with warheads highlighted
- md_parameters: GROMACS MD parameter files for minimization, equilibration, and NPT production simulations