Rubicon
Daylight's 3-D structure generator, available as the program Rubicon
and the Rubicon Toolkit
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
Methodology:
- establish geometric constraints in distance-space
- sample a conformation in that space
- embed it in 3-dimensions while minimizing bounds violations
More information on distance geometry methods
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
Examples of Rubicon rules:
- RULENAME smarts (atomlist) bounds
- 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)
- TORSION a1aaaaa1 (1,2,3,4) 0.0 0.0- Keeps aromatic rings planar
Examples of Rubicon options:
-RUBE_LIMITEVAL--Limit function evaluations allowed per minimization
(rubicon)
-RUBE_NCONFS --Number of conformations generated for each molecule
(rubicon)
-RUBE_OUTPUT_FORMAT-TDT ....... Write output in TDT format,PDB format
Running Rubicon:
Daylight Chemical Information Systems Inc.