Rubicon

Rubicon(RUle Based Invention of Conformation) is a distance geometry program which uses constraints from a SMARTS-based,rule-driven front end.

Applications:

• 3D structure generation from 2D connectivities
• 3D structure generation with contstraints from training set of known 3D structures
• 3D structure generation within a pharmacophore model

• establish geometric constraints in distance-space
• sample a conformation in that space
• embed it in 3-dimensions while minimizing bounds violations

The Rules/Constraints...

• Default Ruleset: $DY_ROOT/data/rubicon.rules
• Generate ruleset from a known set of 3D structures: autorules
• Make up your own, e.g pharamcophore model

• Syntax: RULENAME smarts (atomlist) bounds
• Example: DISTANCE c:o (1,2) 1.324 1.402
  Sets the bond length bounds for bonds betwee all aromatic carbon and oxygen to the range (1.324-1.402)
• Example: TORSION a1aaaaa1 (1,2,3,4) 0.0 0.0
  Keeps aromatic rings planar

• -RUBE_RULES ... rules file
• -RUBE_LIMITEVAL ... Limit function evaluations allowed per minimization
• -RUBE_NCONFS ... Number of conformations generated for each molecule
• -RUBE_OUTPUT_FORMAT ... TDT or PDB format
• -RUBE_HYDROGENS ... ALL, SOME or NONE
• Enter: rubicon -options for full list

• default rule set, default options

  rubicon [options] < input.tdt > output.tdt

• generate rule set from molecular training set

  autorules [options] < input.tdt > output.rules
rubicon -RUBE_RULES output.rules < input.tdt > output.tdt