Vaidehi Lab Publications

  1. Lee, S., Nivedha, A. K., Tate, C. G., & Vaidehi, N. (2019). Dynamic Role of the G Protein in Stabilizing the Active State of the Adenosine A2A Receptor. Structure, 27:1-10.
  2. Suno R, Lee S, Maeda S, Yasuda S, Yamashita K, Hirata K, Horita S, Tawaramoto MS, Tsujimoto H, Murata T, Kinoshita M, Yamamoto M, Kobilka BK, Vaidehi N, Iwata S, Kobayashi T. 2018, Structural Insights into the subtype-selective antagonists binding to the M2 muscarinic receptor, Nat Chem Biol. 14(12):1150-1158.
  3. Ghosh S, Bierig T, Lee S, Jana S, Löhle A, Schnapp G, Tautermann CS, Vaidehi N. 2018, Engineering Salt Bridge Networks between Transmembrane Helices Confers Thermostability in G-Protein-Coupled Receptors, J Chem Theory Comput. 2018 Nov 6. doi: 10.1021/acs.jctc.8b00602
  4. Tautermann CS, Binder F, Büttner FH, Eickmeier C, Fiegen D, Gross U, Grundl MA, Heilker R, Hobson S, Hoerer S, Luippold A, Mack V, Montel F, Peters S, Bhattacharya S, Vaidehi N, Schnapp G, Thamm S, Zeeb M. 2018, Allosteric Activation of Striatal-Enriched Protein Tyrosine Phosphatase (STEP, PTPN5) by a Fragment-like Molecule, J Med Chem. Sep 12.
  5. Ma N, Lippert LG, Devamani T, Levy B, Lee S, Sandhu M, Vaidehi N, Sivaramakrishnan S. 2018, Bitopic Inhibition of ATP and Substrate Binding in Ser/Thr Kinases through a Conserved Allosteric Mechanism, Biochem., 57(45):6387-6390
  6. Bhargava R, Sandhu M, Muk S, Lee G, Vaidehi N, Stark JM. 2018 C-NHEJ without indels is robust and requires synergistic function of distinct XLF domains, Nat. Commun., 9(1):2484. doi: 10.1038/s41467-018-04867-5
  7. Nivedha AK, Tautermann CS, Bhattacharya S, Lee S, Casarosa P, Kollak I, Kiechle T, Vaidehi N. Identifying Functional Hotspot Residues for Biased Ligand Design in G-protein-coupled Receptors. Molecular pharmacology. 2018 Apr 1;93(4):288-96.
  8. Li H, Sandhu M, Malkas LH, Hickey RJ, Vaidehi N. How Does the Proliferating Cell Nuclear Antigen Modulate Binding Specificity to Multiple Partner Proteins? Journal of chemical information and modeling. 2017 Nov. 57, 12, 3011-3021.
  9. Lee S, Devamani T, Song HD, Sandhu M, Larsen A, Sommese R, Jain A, Vaidehi N, Sivaramakrishnan S. Distinct structural mechanisms determine substrate affinity and kinase activity of protein kinase Cα. Journal of Biological Chemistry. 2017 Sep 29;292(39):16300-9.
  10. Choy C, Ansari KI, Neman J, Hsu S, Duenas MJ, Li H, Vaidehi N, Jandial R. Cooperation of neurotrophin receptor TrkB and Her2 in breast cancer cells facilitates brain metastases. Breast Cancer Research. 2017 Dec;19(1):51.
  11. Krumm BE, Lee S, Bhattacharya S, Botos I, White CF, Du H, Vaidehi N, Grisshammer R. Structure and dynamics of a constitutively active neurotensin receptor. Scientific reports. 2016 Dec 7;6:38564.
  12. Lee S, Mao A, Bhattacharya S, Robertson N, Grisshammer R, Tate CG, Vaidehi N. How do short chain nonionic detergents destabilize G-protein-coupled receptors?. Journal of the American Chemical Society. 2016 Nov 15;138(47):15425-33.
  13. Vaidehi N, Bhattacharya S. Allosteric communication pipelines in G-protein-coupled receptors. Current opinion in pharmacology. 2016 Oct 1;30:76-83.
  14. Bhattacharya S, Salomon-Ferrer R, Lee S, Vaidehi N. Conserved mechanism of conformational stability and dynamics in G-protein-coupled receptors. Journal of chemical theory and computation. 2016 Oct 17;12(11):5575-84.
  15. Semack A, Sandhu M, Malik RU, Vaidehi N, Sivaramakrishnan S. Structural Elements in the Gαs and Gαq C Termini That Mediate Selective G Protein-coupled Receptor (GPCR) Signaling. Journal of Biological Chemistry. 2016 Aug 19;291(34):17929-40.
  16. Kandel S, Salomon-Ferrer R, Larsen AB, Jain A, Vaidehi N. 2016, Overcoming potential energy distortions in constrained internal coordinate molecular dynamics simulations, J. Chem. Phys. 144, 044112.
  17. Vaidehi N, Grisshammer R, Tate CG. 2016, How can Mutations Thermostabilize G-protein-coupled receptors? Trends Pharmcol. Sci. 37, 37-46. 
  18. Lee S, Heinrich EL, Li L, Lu J, Choi AH, Levy RA, Wagner JE, Yip ML, Vaidehi N, Kim J. 2015, CCR9-mediated signaling through β-catenin and identification of a novel CCR9 antagonist, Mol. Oncol. 9, 1599-611. 
  19. Soto AG, Smith TH, Chen B, Bhattacharya S, Cordova IC, Kenakin T, Vaidehi N. Trejo J. 2015, N-linked glycosylation of protease-activated receptor-1 at extracellular loop 2 regulates G-protein signaling bias, Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):E3600-8.
  20. Lee, S., Bhattacharya S., Tate C.G., Grisshammer R and Vaidehi N. 2015, Structural Dynamics and Thermostabilization of Neurotensin Receptor 1, J. Phys. Chem B, 119(15):4917-28.
  21. Yu DD. Sousa KM, Mattern DL. Wagner JE, Fu X, Vaidehi N. Forman B.M., and Huang W., 2015, Stereoselective synthesis, biological evaluation, and modeling of novel bile acid derived G-protein coupled bile acid receptor (GP-BAR1, TGR5) agonists, Bioorg Med Chem 23, 1613-28.
  22. Vaidehi N, and Jain A. 2015, Internal Coordinate molecular dynamics: a foundation for multiscale dynamics, J. Phys. Chem B 119, 1233-42. Featured article
  23. Nedjai B, Viney JM, Li H, Hull C, Anderson CA, Horie T, Horuk R, Vaidehi N, Pease JE. 2015, CXCR3 antagonist VUF10085 binds to an intrahelical site distinct from that of the broad spectrum antagonist TAK-779, Br J Pharmacol. 172(7):1822-1833.
  24. Bhattacharya S, Lee S, Grisshammer R, Tate CG, Vaidehi N. 2014, Rapid Computational Prediction of Thermostabilizing Mutations for G Protein-Coupled Receptors, J. Chem Theory Comput. 2014 Nov 11;10(11):5149-5160.
  25. Muppidi J, Schmitz Green J, Xiao W, Larsen AB, Braun S., An J, Xu Y, Rosenwald A, Ott G, Gascoyne R, Rimsza L, Campo E, Jaffe E, Delabie J, Smeland E, Braziel, R, Tubbs R, Cook J., Weisenburger D, Chan W, Vaidehi N, Staudt L, Cyster J. 2014, Loss of signaling via Gα13 in germinal center Bcell derived Lymphoma, Nature, 516(7530):254-8.
  26. Larsen AB, Wagner JR, Kandel S, Salomon-Ferrer R, Vaidehi N, Jain A. 2014, GneimoSim: A modular internal coordinates molecular dynamics simulation package,  J Comput Chem. 5(31):2245-55.
  27. Bhattacharya S, and Vaidehi N. 2014, Differences in allosteric communication pipelines in the inactive and active states of a GPCR, BioPhys. J., 107, 422-34. Recognized as New and Notable by the Biophysical Society. 
  28. Li H, Kasam V, Tautermann CS, Seeliger D, Vaidehi N. 2014, Computational method to identify druggable binding sites that target protein-protein interactions, J. Chem. Inf. Model 54, 1391-400. 
  29. Lee S, Bhattacharya S, Grisshammer R, Tate C, Vaidehi N. 2014, Dynamic Behavior of the Active and Inactive States of the Adenosine A2A Receptor.J Phys Chem B. 118(12):3355-65.
  30. Neman J, Termini J, Wilczynski S, Vaidehi N, Choy C, Kowolik CM, Li H, Hambrecht AC, Roberts E, Jandial R. 2014, Human breast cancer metastases to the brain display GABAergic properties in the neural niche, Proc. Natl. Acad. Sci., USA, 111, 984-9.
  31. Larsen AB, Wagner JR, Jain A, Vaidehi N. 2014, Protein Structure Refinement of CASP target Proteins suing GNEIMO torsional dynamics method, J. Chem. Inf. Model. 2014  24;54(2):508-17.
  32. Vaidehi N, Bhattacharya S, Larsen AB. 2014, Structure and dynamics of G-protein coupled receptors, Adv. Exp. Med. Biol., 796, 37-54. 
  33. Jain A, Kandel S, Wagner JE, Larsen AB, Vaidehi N. 2013, Fixman compensating potential for general branched molecules, J. Chem. Phys. 139, 244103-. 
  34. Niesen MJM, Bhattacharya S, Grisshammer R, Tate CG, Vaidehi N, 2013, Thermostabilization of the β1-adrenergic receptor correlates with increased entropy of the inactive state, J. Phys. Chem B, 117, 7283-91.
  35. Gangupomu VK, Wagner JR, Park IH, Jain A, Vaidehi N., 2013, Mapping conformational dynamics of proteins using torsional dynamics simulations, Biophys. J., 104, 1999-2008.
  36. Wagner JR, Balaraman GS, Niesen MJ, Larsen AB, Jain A, Vaidehi N. 2013, Advanced techniques for constrained internal coordinate molecular dynamics, J Comput Chem. 34(11):904-14
  37. Jain A, Park IH, Vaidehi N. 2012, Equipartition principle for internal coordinate molecular dynamics,  J Chem Theory Comput. 14;8(8):2581-2587.
  38. Bhattacharya S, Lam AR, Li H, Balaraman G, Niesen MJ, Vaidehi N. 2013, Critical analysis of the successes and failures of homology models of G protein-coupled receptors, Proteins. 81(5):729-39. 
  39. Bhattacharya S., Vaidehi N. 2012, LITiCon: a discrete conformational sampling computational method for mapping various functionally selective conformational states of transmembrane helical proteins. Methods. Mol. Biol., 914, 167-78. 
  40. Pascal TA, Goddard WA 3rd, Maiti PK, Vaidehi N. 2012, Role of specific cations and water entropy on the stability of branched DNA motif structures J Phys Chem B.  11;116(40):12159-67. 
  41. Fowler JC, Bhattacharya S, Urban JD, Vaidehi N, Mailman RB. 2012, Receptor Conformations Involved in Dopamine D2L Receptor Functional Selectivity Induced by Selected Transmembrane 5 Serine Mutations., Mol. Pharm., 81(6):820-31.
  42. Vaidehi, N, Klein-Seetharaman J. 2012, Membrane Protein Structure Determination, Editor for Methods in Mol. Biol. Volume 914.
  43. Kim J, Li H, Hsin C, Yip RL. and Vaidehi, N., 2012, Identification of antimalarial compounds as novel antagonists to CXCR4 in pancreatic cancer cells, Plos One, 7, e31004. 
  44. Park IH, Wagner J, Jain A, Vaidehi N. 2012, Structure Refinement of Protein Low Resolution Models Using the GNEIMO Constrained Dynamics Method Folding of Small Proteins Using Constrained Molecular Dynamics, J.  Phys. Chem. B, 116, 2365-75.
  45. Lin J, Liu P, Yang HZ, Vaidehi N. 2012, Factors that affect the computational prediction of hot spots in protein-protein complexes, Comp. Mol. Bioscience, 2, 
  46. Nedjai B., et al. 2012, Small molecule chemokine mimetics suggest a molecular basis for the observation that CXCL10 and CXCL11 are allosteric ligands of CXCR3, Br. J. Pharmacol. 166(3):912-23. 
  47. Vaidehi N, Bhattacharya S. 2011 Multiscale computational methods for mapping conformational ensembles of G-protein coupled receptors, Adv. Protein Chem. Struct. Biol., 85, 253-80.
  48. Niesen MJM, Bhattacharya S, Vaidehi N. 2011 The Role of Conformational Ensembles in Ligand Recognition in G-Protein Coupled Receptors. J. Am. Chem. Soc. 133(33):13197-204.
  49. Lu RZ, Niesen MJM, Hu WD, Vaidehi N, Shively JE. 2011, Interaction of Actin with Carcinoembryonic Antigen-related Cell Adhesion Molecule 1 (CEACAM1) Receptor in Liposomes Is Ca(2+)- and Phospholipid-dependent. Journal of Biological Chemistry. 286(31):27528-36.
  50. 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. 51(1), 139-47.
  51. Buettner R, Corzano R, Rashid R, Lin JP, Senthil M, Hedvat M, et al. 2011, Alkylation of Cysteine 468 in Stat3 Defines a Novel Site for Therapeutic Development. ACS Chemical Biology. 6(5):432-43.
  52. Balaraman GS, Park IH, Jain A, Vaidehi N. 2011, Folding of Small Proteins Using Constrained Molecular Dynamics. Journal of Physical Chemistry B. 115(23):7588-96.
  53. Vaidehi N, Kenakin T. 2010, The role of conformational ensembles of seven transmembrane receptors in functional selectivity. Current Opinion in Pharmacology. 10(6):775-81. Invited review
  54. Vaidehi N. 2010, Dynamics and flexibility of G-protein-coupled receptor conformations and their relevance to drug design. Drug Discovery Today.;15(21-22):951-7.
  55. Spijker P, van Hoof B, Debertrand M, Markvoort AJ, Vaidehi N, Hilbers PAJ. 2010, Coarse Grained Molecular Dynamics Simulations of Transmembrane Protein-Lipid Systems. Int. J.  Mol. Sci. 2010;11(6):2393-420.
  56. Bhattacharya S, 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.
  57. Bhattacharya S, Subramanian G, Hall S, Lin JP, Laoui A, Vaidehi N. 2010, Allosteric antagonist binding sites in class B GPCRs: corticotropin receptor 1. J. Computer-Aided Mol. Des., 24(8):659-74.
  58. Balaraman GS, Bhattacharya S, Vaidehi N. 2010, Structural insights into conformational stability of wild-type and mutant β1-adrenergic receptor Biophys. J., 99, 568-77. 
  59. Vaidehi N, Pease JE, Horuk R. 2009, Modeling Small Molecule-Compound Binding to G-Protein-Coupled Receptors. Chemokines, Pt A., Methods in Enzym., 460, 263-88.
  60. Lin JP, Buettner R, Yuan YC, Yip R, Horne D, Jove R, et al. 2009, Molecular dynamics simulations of the conformational changes in signal transducers and activators of transcription, Stat1 and Stat3. J. Molec. Graph. & Model, 28(4):347-56.
  61. Hall SE, Roberts K, Vaidehi N. 2009, Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction. J.  Mol. Graph. & Model., 27(8):944-50.
  62. Hall SE, Mao A, Nicolaidou V, Finelli M, Wise EL, Nedjai B, et al. 2009, Elucidation of Binding Sites of Dual Antagonists in the Human Chemokine Receptors CCR2 and CCR5. Molecular Pharmacology, 75(6):1325-36.
  63. Lin JP, Seeman NC, Vaidehi N. 2008, Molecular-dynamics simulations of insertion of chemically modified DNA nanostructures into a water-chloroform interface. Biophysical Journal, 95(3):1099-107.
  64. Bhattacharya S, Hall SE, Vaidehi N. 2008, Agonist-induced conformational changes in bovine rhodopsin: Insight into activation of G-protein-coupled receptors. Journal of Molecular Biology, 382(2):539-55.
  65. Bhattacharya S, Hall SE, Li H, Vaidehi N.2008, Ligand-stabilized conformational states of human beta(2) adrenergic receptor: Insight into G-protein-coupled receptor activation. Biophysical Journal, 94(6):2027-42.
  66. Yanamala NVK, Tirupula KC, Nadella K, Nagarajan V, Klein-Seetharaman J. 2007, Modeling of structure and binding site of allosteric modulators of metabotropic glutamate, receptors. Biophysical Journal, 5a-a.
  67. Ryman-Rasmussen JP, Griffith A, Oloff S, Vaidehi N, Brown JT, Goddard WA, et al. 2007, Functional selectivity of dopamine D(1) receptor agonists in regulating the fate of internalized receptors. Neuropharmacology, 52(2):562-75.
  68. Maiti PK, Pascal TA, Vaidehi N, Goddard WA. 2007, Understanding DNA based nanostructures. Journal of Nanoscience and Nanotechnology, 7(6):1712-20.
  69. Li YY, Zhu FQ, Vaidehi N, Goddard WA, Sheinerman F, Reiling S, et 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, 129(35):10720-31.
  70. Heo J, Vaidehi N, Wendel J, Goddard WA. 2007, Prediction of the 3-D structure of rat MrgA G protein-coupled receptor and identification of its binding site. Journal of Molecular Graphics & Modelling, 26(4):800-12.
  71. Heo J, Han SK, Vaidehi N, Wendel J, Kekenes-Huskey P, Goddard WA. 2007, Prediction of the 3D structure of FMRF-amide neuropeptides bound to the mouse MrgC11 GPCR and experimental validation. Chembiochem, 8(13):1527-39.
  72. Vaidehi N, Schlyer S, Trabanino RJ, Floriano WB, Abrol R, Sharma S, et al. 2006, Predictions of CCR1 chemokine receptor structure and BX 471 antagonist binding followed by experimental validation. Journal of Biological Chemistry, 281(37):27613-20.
  73. Trabanino RJ, Vaidehi N, Goddard WA. 2006, Exploring the molecular mechanism for color distinction in humans. Journal of Physical Chemistry B, 110(34):17230-9.
  74. Spijker P, Vaidehi N, Freddolino PL, Hilbers PAJ, Goddard WA. 2006, Dynamic behavior of fully solvated beta 2-adrenergic receptor, embedded in the membrane with bound agonist or antagonist. Proc. Natl. Acad. Sci. USA, 103(13):4882-7.
  75. Peng JYC, Vaidehi N, Hall SE, Goddard WA. 2006, The predicted 3D structures of the human M1 muscarinic acetylcholine receptor with agonist or antagonist bound. Chemmedchem, 1(8):878-90.
  76. McClendon CL, Vaidehi N, Kam VWT, Zhang DQ, Goddard WA. 2006, Fidelity of seryl-tRNA synthetase to binding of natural amino acids from HierDock first principles computations. Protein Engineering Design & Selection, 19(5):195-203.
  77. Maiti PK, Pascal TA, Vaidehi N, Heo J, Goddard WA. 2006, Atomic-level simulations of Seeman DNA nanostructures: The paranemic crossover in salt solution. Biophysical Journal, 90(5):1463-79.
  78. Gama CI, Tully SE, Sotogaku N, Clark PM, Rawat M, Vaidehi N, et al. 2006, Sulfation patterns of glycosaminoglycans encode molecular recognition and activity. Nature Chemical Biology, 2(9):467-73.
  79. Floriano WB, Hall S, Vaidehi N, Kim U, Drayna D, Goddard WA. 2006, Modeling the human PTC bitter-taste receptor interactions with bitter tastants. Journal of Molecular Modeling, 12(6):931-41.
  80. Vaidehi N, Kalani YS, Hall SE, Freddolino PL, Trabanino RJ, Floriano WB, et al. 2005, First principles structure and function prediction for G-protein coupled receptors. Biophysical Journal, 88(1):357A-A.
  81. Hummel P, Vaidehi N, Floriano WB, Hall SE, Goddard WA. 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, 14(3):703-10.
  82. Cho AE, Wendel JA, Vaidehi N, Kekenes-Huskey PM, Floriano WB, Maiti PK, et al. 2005, The MPSim-Dock hierarchical docking algorithm: Application to the eight trypsin inhibitor cocrystals. Journal of Computational Chemistry, 26(1):48-71.
  83. Trabanino RJ, Hall SE, Vaidehi N, Floriano WB, Kam VWT, Goddard WA. 2004, First principles predictions of the structure and function of G-protein-coupled receptors: Validation for bovine rhodopsin. Biophysical Journal, 86(4):1904-21.
  84. Rogstad DK, Heo J, Vaidehi N, Goddard WA, Burdzy A, Sowers LC. 2004, 5-formyluracil-induced perturbations of DNA function. Biochemistry, 43(19):5688-97.
  85. Maiti PK, Pascal TA, Vaidehi N, Goddard WA. 2004, The stability of Seeman JX DNA topoisomers of paranemic crossover (PX) molecules as a function of crossover number. Nucleic Acids Research, 32(20):6047-56.
  86. Kalani MYS, Vaidehi N, Hall SE, Trabanino RJ, Freddolino PL, Kalani MA, et 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, 101(11):3815-20.
  87. Hall SE, Floriano WB, Vaidehi N, Goddard WA. 2004, Predicted 3-D structures for mouse 17 and rat 17 olfactory receptors and comparison of predicted odor recognition profiles with experiment. Chemical Senses, 29(7):595-616.
  88. Freddolino PL, Kalani MYS, Vaidehi N, Floriano WB, Hall SE, Trabanino RJ, et al. 2004, Predicted 3D structure for the human beta 2 adrenergic receptor and its binding site for agonists and antagonists. Proceedings of the National Academy of Sciences of the United States of America, 101(9):2736-41.
  89. Floriano WB, Vaidehi N, Zamanakos G, Goddard WA. 2004, HierVLS hierarchical docking protocol for virtual ligand screening of large-molecule databases. Journal of Medicinal Chemistry, 47(1):56-71.
  90. Floriano WB, Vaidehi N, Goddard WA. 2004, Making sense of olfaction through predictions of the 3-D structure and function of olfactory receptors. Chemical Senses, 29(4):269-90.
  91. Datta D, Vaidehi N, Zhang DQ, Goddard WA. 2004, Selectivity and specificity of substrate binding in methionyl-tRNA synthetase. Protein Science, 13(10):2693-705.
  92. Wintrode PL, Zhang DQ, Vaidehi N, Arnold FH, Goddard WA. 2003, Protein dynamics in a family of laboratory evolved thermophilic enzymes. Journal of Molecular Biology, 327(3):745-57.
  93. Kekenes-Huskey PM, Vaidehi N, Floriano WB, Goddard WA. 2003, Fidelity of phenylalanyl-tRNA synthetase in binding the natural amino acids. Journal of Physical Chemistry B, 107(41):11549-57.
  94. Datta D, Vaidehi N, Floriano WB, Kim KS, Prasadarao NV, Goddard WA. 2003, 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(2):213-21.
  95. Zhang DQ, Vaidehi N, Goddard WA, Danzer JF, Debe D. 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, 99(10):6579-84.
  96. Wang P, Vaidehi N, Tirrell DA, Goddard WA. 2002, Virtual screening for binding of phenylalanine analogues to phenylalanyl-tRNA synthetase. Journal of the American Chemical Society, 124(48):14442-9.
  97. Vaidehi N, Floriano WB, Trabanino R, Hall SE, Freddolino P, Choi EJ, et 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, 99(20):12622-7.
  98. Datta D, Vaidehi N, Xu X, Goddard WA. 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, 99(5):2636-41.
  99. Tang Y, Ghirlanda G, Vaidehi N, Kua J, Mainz DT, Goddard WA, et al. 2001, Stabilization of coiled-coil peptide domains by introduction of trifluoroleucine. Biochemistry, 40(9):2790-6.
  100. Goddard WA, Cagin T, Blanco M, Vaidehi N, Dasgupta S, Floriano W, et al. 2001, Strategies for multiscale modeling and simulation of organic materials: polymers and biopolymers. Computational and Theoretical Polymer Science, 11(5):329-43.
  101. Higgins G, Athey B, Bassingthwaighte J, Burgess J, Champion H, Cleary K, Dev P, Duncan J, Hopmeier M, Jenkins D, Johnson C, Kelly H, Leitch R, Lorensen W, Metaxas D, Spitzer V, Vaidehi N, Vosburgh K, Winslow R. 2001, “Modeling and Simulation in Medicine: Towards an integrated framework, Comput Aided Surg, 6(1):32-9. 
  102. Cagin T, Wang GF, Martin R, Zamanakos G, Vaidehi N, Mainz DT, et al. 2001, Multiscale modeling and simulation methods with applications to dendritic polymers. Computational and Theoretical Polymer Science, 11(5):345-56.
  103. Vaidehi N, Goddard WA. 2000, Domain motions in phosphoglycerate kinase using hierarchical NEIMO molecular dynamics simulations. Journal of Physical Chemistry A, 104(11):2375-83.
  104. Floriano WB, Vaidehi N, Goddard WA, Singer MS, Shepherd GM. 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, 97(20):10712-6.
  105. Bertsch RA, Vaidehi N, Chan SI, Goddard WA. 1998, Kinetic steps for alpha-helix formation. Proteins-Structure Function and Bioinformatics, 33(3):343-57.
  106. Vaidehi N, Goddard WA. 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, 94(6):2466-71.
  107. Lim KT, Brunett S, Iotov M, McClurg RB, Vaidehi N, Dasgupta S, et al. 1997,  Molecular dynamics for very large systems on massively parallel computers: The MPSim program. Journal of Computational Chemistry, 18(4):501-21.
  108. Vaidehi N, Jain A, Goddard WA. 1996, Constant temperature constrained molecular dynamics: The Newton-Euler inverse mass operator method. Journal of Physical Chemistry, 100(25):10508-17.
  109. Fowler PW, Kelly HM, Vaidehi N. 1994,  A Model for Multipole Polarizabilities and Dispersion Coefficients. Molecular Physics, 82(1):211-25.
  110. Jain A, Vaidehi N, Rodriguez G. 1993, A Fast Recursive Algorithm for Molecular-Dynamics Simulation. Journal of Computational Physics, 106(2):258-68.
  111. Vaidehi N, Wesolowski TA, Warshel A. 1992, Quantum-Mechanical Calculations of Solvation Free-Energies - a Combined Ab Initio Pseudopotential Free-Energy Perturbation Approach. Journal of Chemical Physics, 97(6):4264-71.
  112. Vijayakumar M, Vaidehi N, Gopinathan MS. 1989, Fermi and Coulomb Correlated Relativistic Local-Density Method for Atoms. Physical Review A, 40(12):6834-51.
  113. Vaidehi N, Akila R, Shukla AK, Jacob KT. 1986, Enhanced Ionic-Conduction in Dispersed Solid Electrolyte Systems Caf2-Al2o3 and Caf2-Ceo2. Materials Research Bulletin, 21(8):909-16.
  114. Shukla AK, Vaidehi N, Jacob KT. 1986, Ionic-Conduction in Dispersed Solid-Electrolytes. Proceedings of the Indian Academy of Sciences-Chemical Sciences, 96(6):533-47.
  115. Vaidehi N, Gopinathan MS. 1984, Ab Initio Local-Density Potential for Atoms - the Modified Xi-Method. Physical Review A, 29(4):1679-90.

Book Chapters

  1. Vaidehi N and Goddard III W.A. 2001, chapter 6, pp 161-188 title "Atomic-Level Simulation and Modeling of Biomacromolecules” in the book titled "Computational Modeling of Genetic and Biochemical Networks” Editors Hamid Bolouri and James M. Bower, MIT Press.
  2. Vaidehi N and Klein-Seetharaman J edited a volume of Methods in Molecular Biology titled "Membrane Protein Structure and Dynamics: Methods and Protocols”  Volume 914, Humana Press 2012. 


"System and methods for predicting transmembrane domains in membrane proteins and mining the genome for recognizing G-protein coupled receptors” US 8370074 B2