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PUBLICATIONS
(The pre-NPEBC participants (Faculty) and their postdocs/students are written in boldface. The publications labeled as (*) refer to developmental projects DP1-DP3 and the other DPs (see Section D)
Aronson Jr., Nathan N.; Halloran, B. A.; Alexyev, M. F.; Amable, L.; Madura, J. D.; Pasupulati, L.; Worth, C.; Van Roey, P. (2004). Mechanism of Chitin Oligosaccharide Hydrolysis by the Family 18 Chitinase A from Serratia marcescens Biochem. J., in press.
Brisson, M., T Nguyen, A Vogt, J Yalowich, A Giorgianni, D Tobi, I Bahar, CRJ Stephenson, P Wipf and JS Lazo. 2004. Discovery and characterization of novel small molecule inhibitors of human Cdc25B dual specificity phosphatase Molecular Pharmacology, (in press). (*)
Chen, S-C. and I Bahar. 2004. Mining frequent patterns in protein structures: a study of protease families. Bioinformatics 20 Suppl. 1, i1-19. (pdf)
Dalal, P.D., Aronson, N.N.Jr., Madura, J.D. (2004). Family 18 Chitolectins: Comparison of MGP40 and GP39. (submitted).
Dalal, P.D., Robertson, K, Aronson, N.N.Jr., Madura, J.D. (2004). Isothermal Calorimetric Study of Oligosaccharide Binding to SmChiA E315L Mutant. (manuscript in preparation).
Dalal, P.D., Thomas, L.L., Robertson K., Halloran, B.A., Aronson, N.N.Jr., Madura, J.D. (2004). Thermodynamic properties of chitinase interaction with oligosaccharides. (submitted).
Graf, P., MG Kurnikova, RD Coalson and A Nitzan. 2004. Comparison of dynamic lattice Monte-Carlo simulations and dielectric self energy Poisson-Nernst-Planck continuum theory for model ion channels. J. Phys. Chem. B 108, 2006-2015. (*) (pdf)
Katpally, S.; Ghorab, M. K., Madura, J. D., Mosher, J., Thompson, D., Adeyeye, M. C. (2004). Characterization of Bile Salt/SBE-7b-cyclodextrin Interactions Using Isothermal Titration Calorimetry, submitted.
Rader, AJ and I. Bahar. 2004. Folding Core Predictions from Network Models of Proteins Polymer, 45, 659-668. (pdf)
Rader, AJ., G. Anderson, B. Isin, H. G. Khorana, I. Bahar, and J. Klein-Seetharaman. 2004. Rhodopsin core residues stabilize the disulfide bond at the interface between transmembrane and extracellular domains. Proc. Natl. Acad Sci USA, 101, 7246-7251 (pdf).
Seki, M., C. Masutani, LW Yang, A Schuffert, S Iwai, I Bahar and R Wood. (2004) High efficiency bypass of DNA damage by a single human DNA polymerase, EMBO J., submitted. (*)
Sluis-Cremer, N., NA Temiz, and I Bahar. (2004) Conformational changes in HIV-1 reverse transcriptase induced by nonnucleoside reverse transcriptase inhibitor binding. Current Research in HIV (in press). (*) (pdf)
Stiles, JR, Ford, WC, Pattillo, JM, Deerinck, TE, Ellisman, MH, Bartol, TM, and Sejnowski, TJ, Spatially realistic computational physiology: past, present, and future, to appear in Parallel Computing: Software Technology, Algorithms, Architectures & Applications, ed. G. Joubert et al., Elsevier Press (2004, in press).
Tsonchev, S., RD Coalson, A Liu and TL Beck. 2004. Flexible Polyelectrolyte Simulations at the Poisson-Boltzmann Level: a Comparison of the Kink-Jump and Multigrid Configurational-Bias Monte Carlo Methods. J. Chem. Phys. 120 , 9817-9821. (pdf)
Temiz, A., E. Meirovitch and I. Bahar. 2004. E. coli Adenylate Kinase Dynamics: Comparison of Elastic Network Model Modes with Mode-Coupling 15N-NMR Relaxation Data, Proteins: Structure, Function and Bioinformatics, (in press).
Thomas, L.L., Dalal, P.D., Aronson, N.N.Jr., Madura, J.D. (2004) Molecular Modeling of b(1à4) linked N-acetyl glucosamine in SmChiA Subsites. (manuscript in preparation).
Vodovotz, Y., P Kim, Z Bagci, GB Ermentrout, CC Chow, I Bahar and T. Billiar. 2004. Inflammatory modulation of hepatocyte apoptosis by nitric oxide: in vivo, in vitro, and in silico studies. Current Molecular Medicine, (in press). (*)
Wachman, ES., RE Poage, JR Stiles, DL Farkas and SD Meriney. 2004. Spatial distribution of calcium entry evoked by single action potentials within the presynaptic active zone. J. Neurosci., 24, 2877-2885. (*) (pdf) (appendix)
Wang, Y. Rader, AJ, Bahar, I. and Jernigan, RL. 2004. "Global Ribosome Motions Revealed with Elastic Network Model" J. Struct Biol, (in press).
Wierzbicki, A.; Dalal, P.; Madura, J.D. (2003) Molecular Dynamics Simulations of Crystal Induced Membranolysis J. Phys. Chem. 107, 12345-12351 (pdf).
Xu, C., Dror Tobi and I. Bahar. 2003. Allosteric Changes in Protein Structure Computed by a Simple Mechanical Model: Hemoglobin T --> R2 Transition". J. Mol. Biol. 333, 153–168. (pdf)
Zhou, Z. and Madura, J. D. (2004a) QSAR and CoMFA Study of HIV-RT Inhibitors J. Chem. Inf. Comput. Sci., submitted. (*)
Zhou, Z. and Madura, J. D. (2004b) Relative Free Energy of Binding and Binding Mode Calculations of HIV-1 RT Inhibitors Based on Dock-MM-PB/GS Proteins: Structure, Function and Bioinformatics, in press. (*)
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