RubiconDock engine

• After the ligand is inside all site spheres, the spheres are removed and conjugate gradient minimization continues in 4 dimensions vs. the distance geometry intramolecular error function and an intermolecular steric and electrostatic function:
  
• United atoms with no explicit hydrogens are used; charges are assigned by analogy to AMBER using SMARTS rule-based assignment or by Gasteiger's method.
   
• Docking is scored initially by the final, optimized intermolecular energy.
   
• For ~15 complexes, ~90% of random trials converge with an average CPU time < 0.5 sec/fit (SGI/R10000).

 
• 5 - 10% of the random fits are within 2.5 angstroms RMS of the X-ray crystal structure.

 
• "Energy" scores alone work poorly; other scoring functions are needed.