TGQR 2010Q4 Report.pdf - Teragridforum.org

502. L. Li and T.W. Allen. “Membrane deformations under the actions of lysine and arginine containing
peptides”, in preparation for J. Phys. Chem. B.
503. Vorobyov, I. and T. W. Allen. “The role of anionic lipids in membrane association and translocation
of charged peptides”, in preparation for J. Am. Chem. Soc.
MCB060006
504. Calculation of free energies in fluid membranes subject to heterogeneous curvature fields, N. J.
Agrawal, R. Radhakrishnan, Physical Review E, 80: 011925, 2009. Pubmed ID: 19658747.
505. Computational Delineation of the Catalytic Step of a High Fidelity DNA Polymerase, R.
Venkatramani, R. Radhakrishnan, Protein Science (A Protein Society Journal), 19(4), 815-825, 2010.
Pubmed ID: 20162624.
506. The ErbB3/HER3 Intracellular Domain is Competent to Bind ATP and Catalyze
Autophosphorylation, F. Shi, S. E. Telesco, Y. Liu, R. Radhakrishnan*, M. A. Lemmon*, Proceedings of the
National Academy of Sciences, 2010, in press. Pubmed ID: 20351256; *Co-corresponding authors.
507. Linking oncogenic signaling to molecular structure, Multiscale Cancer Modeling, J. Purvis, A. Shih,
Y. Liu, R. Radhakrishnan, Eds. T.S. Deisboeck, G. Stamatakos, Chapman & Hall-CRC Mathematical and
Computational Biology Series, 2010, in press.
508. Computational methods related to reaction chemistry, A. J. Shih*, S. T. Telesco*, Y. Liu, R.
Venkatramani, R. Radhakrishnan, Comprehensive Biomaterials, eds. P. Ducheyne, Elsevier London, 2010,
in press. *These authors contributed equally.
509. Structural analysis of the activation loop conformation of Epidermal Growth Factor Receptor
Tyrosine Kinase through molecular dynamics simulations, A. Shih, S. H. Choi, M. A. Lemmon, R.
Radhakrishnan, 2009, submitted to Biophsical J.
510. Protein-Mediated Orchestration of Vesiculation Prior to Vesicle-Scission in Clathrin-Dependent
Endocytosis, N. Agrawal, J. Nukpezah, R. Radhakrishnan, 2009, submitted to Plos Computational Biology.
511. A finite element method for simulating thermally fluctuating Brownian particles, B. Uma, T. N.
Swaminathan, R. Radhakrishnan, D. M. Eckmann, P. S. Ayyaswamy, 2010, submitted to Phys. Rev. E.
512. Design of functionalized nanocarriers for endothelial targeting based on Monte Carlo calculations of
absolute free energy of binding, J. Liu, D. M. Eckmann, P. S. Ayyaswamy, V. Muzykantov, R.
Radhakrishnan, 2010, submitted to PNAS.
513. A molecular docking study of the binding of ruthenium complex compounds to PIM1, GSK3, and
CDK2 protein kinases, Y. Liu, N. J. Agrawal, R. Radhakrishnan, 2009, submitted.
514. Mechanisms of phosphoryl transfer in ErbB3 kinase, F. Jia, S. Telesco, Y. Liu, R. Radhakrishnan,
2010, to be submitted.
515. Energy landscapes in tyrosine phosphorylation and mechanisms of phosphoryl transfer in ErbB1
kinase, Y. Liu, R. Radhakrishnan, 2010, to be submitted.
516. Binding of Erlotinib to Inactive ErbB1 tyrosine kinase domain, Y. Liu, J. Park, M. A. Lemmon, R.
Radhakrishnan, 2010, to be submitted.
517. Mechanism of clathrin-mediated vesicle budding in receptor endocytosis, N. J. Agrawal, S. Engles,
R. Toy, R. Radhakrishnan, 2010, to be submitted.
MCB060069
518. Gedeon, P.C.; Indarte, M.; Surratt, C.K.; Madura, J.D. Molecular dynamics of leucine and
dopamine transporter proteins in a model cell membrane lipid bilayer, Proteins, 2010. 78, 797.
519. Asciutto, E.K.; General, I.J.; Xiong, K.; Asher S.A.; and Madura, J.D. Sodium Perchlorate effects on
the helical stability of a mainly alanine peptide. Biophys. J, 2010, 98, 186.
520. Indarte, M; Liu, Y.; Madura, J.D. and Surratt, C.K. Receptor---based discovery of plasmalemmal
monoamine transporter inhibitor via high---throughput docking and pharmacophore modeling. ACS Chemical
Neuroscience, 2010. 1, 223.