Simulations of Biological Macromolecules



Vaidehi Nagarajan, Wely Floriano, Joyce Peng, Derek Debe and William Goddard III












Inhibitors for E.coli invasion of the brain microvascular endothelial cells











OmpA binding Studies


Crystal Structure of OmpA.

Possible Binding Pockets in OmpA.


Preliminary Results on Binding


Binding energies (estimate) from Annealing MD simulations

10 cycles of Annealing simulations done from 300 to 600K.

  1. protein fixed and only the ligand and waters movable
  2. all residues within 5A distance from the ligand are movable with ligand and waters.








Restraint Generic Protein_Loop Builder












RGP for Membrane Proteins


  1. Grows loops within 120% of the membrane volume which allows the loops to be within the hydrophobic region.










  1. The angles at the start and the end of the loop are extended(pdb) and biased towards growing it extended for short loops (<15 res).

  3. Longer loops are grown without condition 2 and with condition 1.






RGP Predictions for OmpF short loops

























Structure Prediction, Molecular Dynamics and Function Correlations


Wely Floriano, Vaidehi Nagarajan & William Goddard III (Caltech)

Bettina Malnic & Linda Buck ( Harvard Medical)

Mike Singer & Gordon Shepherd (Yale Medical)









Details will be given in talk D1 (Floriano).















































Heirarchical NEIMO Method

Georgios Zamanakos














H-NEIMO Model for Odor Receptors