Daylight Worksheet - Rubicon--SHOW HINTS

Rubicon, "Rule-Based Invention of Conformations", generates 3D coordinates for a TDT file using a simple set of rules, or rules generated from a training set with autorules.

1. Generate 3D coordinates to the drugs.tdt dataset created in the PCModels exercise or use the drugs.tdt file.
   • List Rubicon options

     rubicon -options

   • List current settings

     rubicon -settings

   • Generate 3D coordinates with standard ruleset

     rubicon < drugs.tdt > drugs.3d.tdt

2. Generate 3D coordinates using rules generated from a training set and autorules. Obtain the training set from a substructural search of the medchem00 database and thorlookup to obtain the $D3D data.
   • Open the medchem00 database in merlin and search for a substructure from the drugs.tdt dataset.

   • Save the search results in a tdt file

   • Use thorlookup to find the $D3D data

   • generate a rule set

     autorules < hitlist.tdt > output.rules

   • Generate 3D structures for drugs.tdt dataset using the new ruleset