Ryman-Rasmussen, J.P., Griffith A., Oloff S., Vaidehi, N., Brown J.T., Goddard W.A., and Mailman R.B., 2007, Functional Selectivity of dopamine D2 receptor agonists in regulating the fate of internalized receptors, Neuropharmacology, 52, 562-575.

Peng, Y.C., Hall, S.E. Goddard III, and Vaidehi N. 2006, The Predicted 3D structures of Human Muscarinic acetylcholine receptor M1 with agonist or antagonist bound, ChemMedChem, 1, 878-890.

Spijker, P., Vaidehi, N., Freddolino P.L, Hilbers, P.A. and Goddard W.A. 2006, Dynamic Behavior of Fully Solvated Beta2-Adrenergic Receptor, Embedded In The Membrane With Bound Agonist or Antagonist, Proc. Natl. Acad. Sci. USA , 103, 4882- 4887.

Vaidehi, N., Schyler S., Trabanino R.J., Floriano, W.B., Abrol, R., Sharma S., Kochanny M., Koovakkat, S., Dunning L., Liang M., Fox J.M. de Mendoca F.L., Pease J., Goddard III, W.A and Horuk R., 2006, Predictions of CCR1 Chemokine Receptor Structure and BX 471 Antagonist Binding Followed By Experimental Validation, J. Biol. Chem. 281(37):27613-20.

Trabanino R.J., Vaidehi, N., and Goddard W.A.  2006, Exploring the molecular mechanism for color distinction in humans, J. Phys. Chem B, 110, 17230-17239.

Cho, A., Wendel, J.A., Vaidehi, N., Kekenes-Huskey, P.M., Floriano, W.B. and Goddard III, Hierarchical Docking Algorithm With Comprehensive Conformational Search And All Atom Forcefield Scoring Function With Solvation: Mpsim-Dock, J. Comp. Chem.  26, 48-71, 2005.

Hummel, P., Vaidehi, N., Floriano, W.B., Hall, S.E., and Goddard III, W.A. Test of the Binding Threshold Hypothesis For Olfactory Receptors: Explanation Of The Differential Binding Of Ketones To The Mouse And Human Orthologs Of Olfactory Receptor 912-93, Prot. Sci. 14, 703-710, 2005.

Floriano, W. B., Vaidehi, N., Zamanakos, G. & Goddard, W. A., III  HIERVLS- Hierarchical docking protocol for virtual ligand screening for large molecule database., J. Med. Chem. 47, 56–71 (2004).

Trabanino, R., Hall, S.E., Vaidehi, N., Floriano, W., Goddard, W.A.; First Principles Prediction of the structure and Function of G protein-coupled receptors: validation for bovine rhodoBiophys. J., 86, 1904-1921, (2004).

Freddolino, P., Kalani, M.Y., Vaidehi, N., Floriano, W., Hall, S.E., Trabanino, R., Kam, V.W.T., Goddard, W.A.; Predicted 3D structure for the human ß2 adrenergic receptor and its binding site for agonists and antagonists. Proc. Natl. Acad. Sci. USA 101, 2736-2741 (2004).

Kalani, M.Y., Vaidehi, N., Hall, S.E., Trabanino, R., Freddolino, P., Kalani, M.A.,Floriano, W.B., Kam, V., Goddard, W.A., Iii; The Predicted 3d Structure Of The Human D2 Dopamine Receptor And The Binding Site And Binding Affinities For Agonists And Antagonists. Proc. Natl. Acad. Sci. USA 101, 3815-3820 ,2004.

Hall,  S.E.,  Floriano, W.B., Vaidehi , N., and William A. Goddard III Predicted 3-D Structures For Mouse I7 And Rat I7 Olfactory Receptors And Comparison Of Predicted Odor Recognition Profiles With Experiment Chem. Senses 29: 595–616, 2004.

Floriano, W.B. Vaidehi, N., Goddard, W.A., III, Making Sense Of Olfaction Through Predictions Of The 3d Structure And Function Of Olfactory Receptor, Chemical Senses, 29, 269-290, 2004.

Datta, D., Vaidehi, N., Zhang, D. And Goddard III, W.A,  Selectivity And Specificity Of Substrate Binding In Methionyl-Trna Synthetase, Protein Sci.  13, 2693-2705, 2004.

Datta, D., Vaidehi, N., Floriano, W.B.,  Kim, K.S., Prasadarao, N.V. and Goddard III, W.A. Interaction of E-coli Outer membrane protein A with sugars on the receptors of the Brain Microvascular Endothelial Cells. Proteins: Structure, Function and Genetics 50, 213-221, 2003.

Kekenes-Huskey, P.M., Vaidehi N., Floriano, W.B., and Goddard III, Fidelity of phenyl alanyl tRNA synthetase, J. Phys. Chem B (2003), 107, 11549-11557.

Structure-based design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase for incorporation of O-methyl-L-tyrosine, D. Zhang, N. Vaidehi, W. A. Goddard III,, J. F.Danzer, and D. Debe, Proc. Natl. Acad. Sci. USA, Vol. 99, 6579-6584, 2002.

Mechanism for antibody catalysis of the oxidation of water by singlet dioxygen , D. Datta, N. Vaidehi, X. Xu, W. A. Goddard III Proc. Natl. Acad. Sci. USA, 99, 2636 2002.

Wang, P., Vaidehi, N., Tirrell, D.A., and Goddard III,  W.A.,  Virtual Screening for Binding of Phenylalanine Analogs to Phenylalanyl- tRNA Synthetase,  J. Am. Chem. Soc.  124, 14442-14449, 2002.

Vaidehi, N., Floriano, W.B.,   Trabanino, R., Hall, S.,  Freddolino, P.,  Choi, E.J. Zamanakos, G., and William A, Goddard III, Structure and Function prediction for G-Protein Coupled Receptors, Proc. Natl. Acad. Sci., USA, 99, 12622-12627, 2002.

Atomic Level Simulation Models for Biological Systems, N. Vaidehi and W. A. Goddard III in "Computational Models of Molecular and Cellular Interaction", Chapter 7, J. Bower and H. Bolouri Editors MIT Press, 2001.

Stabilization of Leucine Zipper Coiled Coils by Introduction of Trifluoroleucine, Y. Tang, G. Ghirlanda, N. Vaidehi, J. Kua, D. T. Mainz, W. A. Goddard III, W. F. DeGrado, D. A. Tirrell, Biochemistry, 40, 2790-2796, 2001.

Large Scale Domain Motions in Phosphoglycerate Kinase using Heirarchical NEIMO Simulations, N.Vaidehi and W. A. Goddard III, J. Phys. Chem. A, 104, 2375, 2000.

Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor W. B. Floriano, N. Vaidehi, M. S. Singer, G. M. Shepherd, and W. A. Goddard III, Proc. Natl. Acad. Sci. USA., 97, 10712-10716, 2000.

Constant temperature constrained molecular dynamics- the Newton Euler Inverse Mass Operator method , N. Vaidehi, A. Jain and W.A. Goddard III, J. Phys. Chem. 1996, 100, pp 10508.

A Fast Recursive Algorithm For Molecular-Dynamics Simulation, Jain A, Vaidehi N, Rodriguez G., J Comput Phys 106: (2) 258-268 Jun 1993.

This is a partial list. Full publications list available upon request. Information on this page may be self-reported and is subject to change at any time. Last updated: 06/08.