2008 Research Reports

BICB 2008/01
Origin of Mutational Effects at the C3 and G8 Positions on Hammerhead Ribozyme Catalysis from Molecular Dynamics Simulations
Tai-Sung Lee and Darrin M. York

BICB 2008/02
Solvent structure and hammerhead ribozyme catalysis
Monika Martick, Tai-Sung Lee, Darrin M. York, and William G. Scott,

BICB 2008/03
Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation
Tai-Sung Lee, Carlos Silva-Lopez, George M. Giambasu, Monika Martick, William G. Scott, and Darrin M. York

BICB 2008/04
Quantum mechanical/molecular mechanical simulation study of the mechanism of Hairpin ribozyme catalysis
Kwangho Nam, Jiali Gao, and Darrin M. York

BICB 2008/05
Contracted auxiliary Gaussian basis integral and derivative evaluation
Timothy J. Giese and Darrin M. York

BICB 2008/06
Charge-dependent model for many-body polarization, exchange and dispersion interactions in hybrid QM/MM calculations
Timothy J. Giese and Darrin M. York

BICB 2008/07
Publications Quantitative Evaluation of Approximate Frequent Pattern Mining Algorithms
Rohit Gupta, Gang Fang, Blaine Field, Michael Steinbach, and Vipin Kumar

BICB 2008/08
Raf and MEK protein kinases are direct molecular targets for the chemopreventive effect of quercetin, a major flavonol in red wine
Lee, K.W., Kang, N.J., Heo, Y.S., Rogozin, E.A., Pugliese, A., Hwang, M.K., Bowden, G.T., Bode, A.M., Lee, H.J. and Dong, Z. (2008)

BICB 2008/09
The resveratrol analogue 3,5,3',4',5'-pentahydroxy-transstilbene inhibits cell transformation via MEK
Lee, K.W., Kang, N.J., Rogozin, E.A., Oh, S.M., Heo, Y.S., Pugliese, A., Bode, A.M., Lee, H.J. and Dong, Z.

BICB 2008/10
High Throughput Computing Validation for Drug Discovery Using the DOCK Program on a Massively Parallel System
Peters, A., M. Lundberg, Lang, T., Sosa, C. P.

BICB 2008/11
iTRAQ reagent-based quantitative proteomic analysis on a linear ion trap mass spectrometer
Griffin TJ, Xie H, Bandhakavi S, Popko J, Mohan A, Carlis JV, and Higgins L.

BICB 2008/12
Statistical analysis of relative labeled mass spectrometry data from complex samples using ANOVA
Oberg, AL, Mahoney, DW, Eckel-Passow, JE, Malone, CJ, Wolfinger, RD, Hill, EG, Cooper, LT, Onuma, OK, Spiro, C, Therneau, TM, and Bergen, HR III

BICB 2008/13
Synthesizing Stochasticity in Biochemical Systems
Fett, B., Bruck, K., and Riedel, M.D.

BICB 2008/14
Module Locking in Biochemical Synthesis
Fett, B., and Riedel, M.D.

BICB 2008/15
Massively Parallel Genomic Sequence Search onthe Blue Gene/P Architecture
Lin, H., Balaji, P., Poole, R., Sosa, C., Ma, X., Feng, W.

BICB 2008/16
A Simple Rank Test to Distinguish Extreme Pathways fromElementary Modes in Metabolic Networks
Jevremovic, D.; Trinh, C.T.; Srienc, F.; Boley, D.L.