Lam AR, Bhattacharya S, Patel K, Hall SE, Mao A, Vaidehi N. 2011 Importance of receptor flexibility in binding of cyclam compounds to the chemokine receptor CXCR4 J Chem Inf Model. 24;51(1):139-47.
Vaidehi N., and Kenakin T., 2010, Conformational Ensembles of Seven Transmembrane Receptors and their Relevance to Functional Selectivity, Curr. Opinion. Pharmacology, in press – invited review.
Vaidehi, N., 2010, Dynamics and Flexibility of G-protein coupled receptor conformations and its relevance to drug design, Drug Discovery Today, 15, 951-957 – invited review.
Vaidehi, N., 2010, Dynamics and Flexibility of G-protein coupled receptor conformations and its relevance to drug design, Drug Discovery Today, in press – invited review.
Bhattacharya et al 2010, Allosteric Antagonist Binding Sites in Class B GPCRs: Corticotropin Receptor 1, J Comput Aided Mol Des. 8, 659-74.
Balaraman, G., Bhattacharya, S., and Vaidehi, N., 2010, Structural insights into conformational stability of wild type and mutant β1-adrenergic receptor, BioPhys. J., 99(2):568-77.
Vaidehi, N., Pease, J. and Horuk R., 2009, Modeling Small Molecule Compound Binding to G-Protein Coupled Receptors, Methods in Enzymology, 460, 263-288 – invited review.
Bhattacharya S, and Vaidehi N. 2010, Computational Mapping of the Conformational Transitions in Agonist Selective Pathways of a G-Protein Coupled Receptor, J Am Chem Soc. 132(14):5205-14.
Lin J, Buettner R, Yuan YC, Yip R, Horne D, Jove R, Vaidehi N. 2009, Molecular dynamics simulations of the conformational changes in signal transducers and activators of transcription, J Mol Graph Model. 28(4):347-56.
Hall S.E., Mao, A. Nicolaidou, V., Finelli, M., Wise, E.L., Nedjai, B., Kanjanapangka, J., Harirchian, P., Chen, D., Selchau, V., Ribeiro, S., Schyler, S., Pease, J.E., Horuk R., and Vaidehi, N. 2009, Elucidation of binding sites of dual antagonists in the human chemokine receptors CCR2 and CCR5. Mol. Pharm. 75, 1325-1336.
Hall, S.E., Roberts, K., and Vaidehi, N., 2009, Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction, J. Mol. Graph. & Mod. 27, 944-950.
Bhattacharya, S., Hall, S.E. and Vaidehi N., 2008, Agonist induced conformational changes in bovine rhodopsin: Insight into activation of G-protein coupled receptors, J. Mol. Biol. 382, 539-555.
Bhattacharya S., Hall S.E., Li H., Vaidehi N. Ligand-stabilized conformational states of human beta(2) adrenergic receptor: insight into G-protein-coupled receptor activation. Biophys J. 2008, 94(6):2027-42.
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.
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: 04/11.
