Vaidehi, Nagarajan

Combined from CaltechAUTHORS

• Lee, Sangbae and Devamani, Titu, el al. (2017) Distinct structural mechanisms determine substrate affinity and kinase activity of protein kinase Cα; Journal of Biological Chemistry; Vol. 292; No. 39; 16300-16309; PMCID PMC5625059; 10.1074/jbc.M117.804781
• Wang, Pin and Vaidehi, Nagarajan, el al. (2015) Virtual Screening for Binding of Phenylalanine Analogues to Phenylalanyl-tRNA Synthetase; Journal of the American Chemical Society; Vol. 124; No. 48; 14442-14449; 10.1021/ja0175441
• Pascal, Tod A. and Goddard, William A., III, el al. (2012) Role of Specific Cations and Water Entropy on the Stability of Branched DNA Motif Structures; Journal of Physical Chemistry B; Vol. 116; No. 40; 12159-12167; 10.1021/jp306473u
• Heo, Jiyoung and Vaidehi, Nagarajan, el al. (2007) Prediction of the 3-D structure of rat MrgA G protein-coupled receptor and identification of its binding site; Journal of Molecular Graphics and Modelling; Vol. 26; No. 4; 800-812; PMCID PMC2151207; 10.1016/j.jmgm.2007.07.003
• Li, Youyong and Zhu, Fangqiang, el al. (2007) Prediction of the 3D Structure and Dynamics of Human DP G-Protein Coupled Receptor Bound to an Agonist and an Antagonist; Journal of the American Chemical Society; Vol. 129; No. 35; 10720-10731; PMCID PMC2535578; 10.1021/ja070865d
• Maiti, Prabal K. and Pascal, Tod A., el al. (2007) Understanding DNA based Nanostructures; Journal of Nanoscience and Nanotechnology; Vol. 7; No. 6; 1712-1720; 10.1166/jnn.2007.704
• Ryman-Rasmussen, Jessica P. and Griffith, Adam, el al. (2007) Functional selectivity of dopamine D_1 receptor agonists in regulating the fate of internalized receptors; Neuropharmacology; Vol. 52; No. 2; 562-575; PMCID PMC1855220; 10.1016/j.neuropharm.2006.08.028
• Vaidehi, Nagarajan and Schyler, Sabine, el al. (2006) Predictions of CCR1 Chemokine Receptor Structure and BX 471 Antagonist Binding Followed by Experimental Validation; Journal of Biological Chemistry; Vol. 281; No. 37; 27613-27620; 10.1074/jbc.M601389200
• Gama, Cristal I. and Tully, Sarah E., el al. (2006) Sulfation patterns of glycosaminoglycans encode molecular recognition and activity; Nature Chemical Biology; Vol. 2; No. 9; 467-473; 10.1038/nchembio810
• Trabanino, Rene J. and Vaidehi, Nagarajan, el al. (2006) Exploring the Molecular Mechanism for Color Distinction in Humans; Journal of Physical Chemistry B; Vol. 110; No. 34; 17230-17239; 10.1021/jp057144q
• McClendon, Christopher L. and Vaidehi, Nagarajan, el al. (2006) Fidelity of seryl-tRNA synthetase to binding of natural amino acids from HierDock first principles computations; Protein Engineering, Design and Selection; Vol. 19; No. 5; 195-203; 10.1093/protein/gzl001
• Spijker, Peter and Vaidehi, Nagarajan, el al. (2006) Dynamic behavior of fully solvated beta2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist; Proceedings of the National Academy of Sciences of the United States of America; Vol. 103; No. 13; 4882-4887; PMCID PMC1458764; 10.1073/pnas.0511329103
• Maiti, Prabal K. and Pascal, Tod A., el al. (2006) Atomic-Level Simulations of Seeman DNA Nanostructures: The Paranemic Crossover in Salt Solution; Biophysical Journal; Vol. 90; No. 5; 1463-1479; PMCID PMC1367300; 10.1529/biophysj.105.064733
• Hummel, Patrick and Vaidehi, Nagarajan, el al. (2005) 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; Protein Science; Vol. 14; No. 3; 703-710; PMCID PMC2279295; 10.1110/ps.041119705
• Maiti, Prabal K. and Pascal, Tod A., el al. (2004) The stability of Seeman JX DNA topoisomers of paranemic crossover (PX) molecules as a function of crossover number; Nucleic Acids Research; Vol. 32; No. 20; 6047-6056; PMCID PMC534617; 10.1093/nar/gkh931
• Datta, Deepshikha and Vaidehi, Nagarajan, el al. (2004) Selectivity and specificity of substrate binding in methionyl-tRNA synthetase; Protein Science; Vol. 13; No. 10; 2693-2705; PMCID PMC2286561; 10.1110/ps.04792204
• Hall, Spencer E. and Floriano, Wely B., el al. (2004) Predicted 3-D Structures for Mouse I7 and Rat I7 Olfactory Receptors and Comparison of Predicted Odor Recognition Profiles with Experiment; Chemical Senses; Vol. 29; No. 7; 595-616; 10.1093/chemse/bjh063
• Rogstad, Daniel K. and Heo, Jiyoung, el al. (2004) 5-Formyluracil-Induced Perturbations of DNA Function; Biochemistry; Vol. 43; No. 19; 5688-5697; 10.1021/bi030247j
• Floriano, Wely B. and Vaidehi, Nagarajan, el al. (2004) Making Sense of Olfaction through Predictions of the 3-D Structure and Function of Olfactory Receptors; Chemical Senses; Vol. 29; No. 4; 269-290; 10.1093/chemse/bjh030
• Trabanino, Rene J. and Hall, Spencer E., el al. (2004) First Principles Predictions of the Structure and Function of G-Protein-Coupled Receptors: Validation for Bovine Rhodopsin; Biophysical Journal; Vol. 86; No. 4; 1904-1921; PMCID PMC1304048; 10.1016/s0006-3495(04)74256-3
• Kalani, M. Yashar S. and Vaidehi, Nagarajan, el al. (2004) The predicted 3D structure of the human D2 dopamine receptor and the binding site and binding affinities for agonists and antagonists; Proceedings of the National Academy of Sciences of the United States of America; Vol. 101; No. 11; 3815-3820; PMCID PMC374327; 10.1073/pnas.0400100101
• Freddolino, Peter L. and Kalani, M. Yashar S., el al. (2004) Predicted 3D structure for the human β2 adrenergic receptor and its binding site for agonists and antagonists; Proceedings of the National Academy of Sciences of the United States of America; Vol. 101; No. 9; 2736-2741; PMCID PMC365690; 10.1073/pnas.0308751101
• Floriano, Wely B. and Vaidehi, Nagarajan, el al. (2004) HierVLS Hierarchical Docking Protocol for Virtual Ligand Screening of Large-Molecule Databases; Journal of Medicinal Chemistry; Vol. 47; No. 1; 56-71; 10.1021/jm030271v
• Kekenes-Huskey, Peter M. and Vaidehi, Nagarajan, el al. (2003) Fidelity of Phenylalanyl-tRNA Synthetase in Binding the Natural Amino Acids; Journal of Physical Chemistry B; Vol. 107; No. 41; 11549-11557; 10.1021/jp034607o
• Wintrode, Patrick L. and Zhang, Deqiang, el al. (2003) Protein Dynamics in a Family of Laboratory Evolved Thermophilic Enzymes; Journal of Molecular Biology; Vol. 327; No. 3; 745-757; 10.1016/S0022-2836(03)00147-5
• Vaidehi, Nagarajan and Floriano, Wely B., el al. (2002) Prediction of structure and function of G protein-coupled receptors; Proceedings of the National Academy of Sciences of the United States of America; Vol. 99; No. 20; 12622-12627; PMCID PMC130510; 10.1073/pnas.122357199
• Zhang, Deqiang and Vaidehi, Nagarajan, el al. (2002) Structure-based design of mutant Methanococcus jannaschii tyrosyl-tRNA synthetase for incorporation of O-methyl-L-tyrosine; Proceedings of the National Academy of Sciences of the United States of America; Vol. 99; No. 10; 6579-6584; PMCID PMC124445; 10.1073/pnas.052150499
• Datta, Deepshikha and Vaidehi, Nagarajan, el al. (2002) Mechanism for antibody catalysis of the oxidation of water by singlet dioxygen; Proceedings of the National Academy of Sciences of the United States of America; Vol. 99; No. 5; 2636-2641; PMCID PMC122400; 10.1073/pnas.052709399
• Tang, Yi and Ghirlanda, Giovanna, el al. (2001) Stabilization of Coiled-Coil Peptide Domains by Introduction of Trifluoroleucine; Biochemistry; Vol. 40; No. 9; 2790-2796; 10.1021/bi0022588
• Vaidehi, Nagarajan and Goddard, William A., III (2001) Atomic-Level Simulation and Modeling of Biomacromolecules; ISBN 0262024810; Computational Modeling of Genetic and Biochemical Networks; 161-188
• Floriano, Wely B. and Vaidehi, Nagarajan, el al. (2000) Molecular mechanisms underlying differential odor responses of a mouse olfactory receptor; Proceedings of the National Academy of Sciences of the United States of America; Vol. 97; No. 20; 10712-10716; PMCID PMC27088; 10.1073/pnas.97.20.10712
• Vaidehi, Nagarajan and Goddard, William A., III (2000) Domain Motions in Phosphoglycerate Kinase using Hierarchical NEIMO Molecular Dynamics Simulations; Journal of Physical Chemistry A; Vol. 104; No. 11; 2375-2383; 10.1021/jp991985d
• Vaidehi, Nagarajan and Goddard, William A., III (1997) The pentamer channel stiffening model for drug action on human rhinovirus HRV-1A; Proceedings of the National Academy of Sciences of the United States of America; Vol. 94; No. 6; 2466-2471; PMCID PMC20111; 10.1073/pnas.94.6.2466
• Vaidehi, Nagarajan and Jain, Abhinandan, el al. (1996) Constant Temperature Constrained Molecular Dynamics:  The Newton−Euler Inverse Mass Operator Method; Journal of Physical Chemistry; Vol. 100; No. 25; 10508-10517; 10.1021/jp953043o