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Table 3 Arguments of virtual-screening scripts

From: Open-source platform to benchmark fingerprints for ligand-based virtual screening

Step    Input (required)     Input (optional) Output
  Key Description Key Description Description
Scoring -f file containing fp names -o output path for each target, a list
    -a append the output file with (fp name,
      list of 50 scored lists);
  -n number of query molecules -s similarity measure (default: Dice) each scored list
      contains (similarity,
      internal ID, active/inactive)
Validation -m file containing the evaluation -o output path for each target,
   methods and their parameters -i input path(s) a dictionary of methods;
    -r file containing fingerprints to ignore for each method,
      a dictionary of fps;
      for each fp, a list with
      (performance value, rank)
Analysis    -o output path for each target, a table
    -i input path with average performance per fp
      (columns) and method (rows);
      a file with average rank per fp
      (columns) and method (rows);
      a file with pairwise tests
  1. Input and output arguments for the three steps of the virtual-screening (VS) experiment. Fingerprint is abbreviated by fp.