Algorithms Devised and Implemented by
Thomas P. Stockfisch

• Substructure Searching
  • extension of unique smiles to handle zeolites cages
  • core substructure search algorithm and extension to handle zeolite crystals
• QSAR/QSPR statistical modeling
  • decision tree display coordinate calculation that conserves screen real estate
  • non-linear pls-analog neural net architecture for QSAR
  • accommodating missing X data for neural nets
  • accommodating missing Y data for neural nets
  • sensitivity analysis for neural nets
  • improved minimizer (weight control) technique for neural nets
  • automated cost-weighting of predictions among categorical, fingerprint, numeric, missing X, missing Y, and replicated X.
  • multiple Y RP
    • nodes near root apply to all properties
    • nodes near leaves apply to one property
    • useful for elucidating drug selectivity
  • chart-ahead RP
    • alternative branching explored
    • solves exclusive-or problem
• Force Field Development
  • reduction of parameter correlation using penalty function
  • explicit partial charge assignment of heterocycles using substructure lookup
  • “implied scale factor” method of force constant scaling
  • new “distort” method that avoids all close contacts and gives a uniform and complete sampling of desired bond and angle ranges
  • robust and efficient torsional barrier geometry optimization
  • data-base analysis of missing parameters to guide force field research
  • “grid” computing for sgi's
    • keyboard/user activity detection
    • automatic suspension and swapping from memory whenever user activity detected
  • extension of force field terms to cover variable bond orders
  • protocol for automated derivation of bifunctional torsions