Under Construction

Supplementary data accompanying the paper:

"Discovering Rules for protein-ligand specificity using support vector inductive logic programming"

Progol may be downloaded here

SVM light may be downloaded here

The main progol program used for learning rules in this paper can be found in version_1.pl

Other files required include:

  • protein_list_training.pl - List of training dataprotein identifiers used for training
  • fad_training.pl - Pairwise distance info for FAD binding sites
  • nad_training.pl - Pairwise distance info for NAD binding sites
  • posneg_training_reversed.pl - Positive/negative example assignment
  • amino_properties3.pl - Simple biophysical properties of the amino acids

    To learn the rules for this leave-one-out replicate, one would run:

     progol version_1.pl

    The top 1000 rules produced for this run are available in 1000_rules.pl